What do you want to have happen? Seriously, there is enough variety with weapons and weapon conditions that you can justify pretty much anything, as long as we know what you want to happen in the story.
If you *want* the SS to hear him as he gets ready to fire, have him carry a rifle or pistol with an empty chamber. They could conceivably than hear him work the action (run the slide on the pistol or work the bolt on the rifle) when he loads the chamber. He could also make noise some other way, like by bumping into something, creaky floors, etc.
This is not too unrealistic. In many cases it is easier to do the gross manipulation required to work the action to load the chamber under stress than it would be to do the precise action needed to take off the safety.
Don't forget as a partisan he likely doesn't have any real military training so he may be more comfortable carrying with an empty chamber until he knows he needs to shoot.
On the other hand, if you want him to be noiseless and totally surprise the Germans, have him have the rifle or pistol or submachine gun ready to go. No safety, just ready to fire. Figure then he worked the action to chamber the round just *before* they entered the church so they wouldn't hear it. Then all that is involved is point and shoot.
If he's up against two SS, and you need him to win, I'd arm him with a captured MP 40 submachine gun as well. The scenario would go something like this:
The partisan sees the SS approaching or sees the SS rounding up citizens outside (whatever) so he finds a good hiding spot in the church where he can watch the door. (Maybe up in a balcony/choir loft or something? People tend not to look up right away in a fight and that would give him an advantage)
The partisan needs to make his weapon ready. With a MP 40 submachine gun he likely would already have a magazine inserted with the bolt handle pulled back to second (closest to the back end) safety notch. This puts the bolt to the rear, but the weapon can not yet be fired. What he'd do to ready it to fire is grab the bolt handle, rotate it down (out of the safety notch) and put it in the main cut out (where the bolt handle travels)in the receiver. When he lets go of the bolt handle the bolt will go forward a couple inches until it stops at the "ready to fire" notch. (The bolt is still all the way to the rear, but because the bolt handle is no longer in the safety notch when the trigger is pressed the bolt will be released to fly forward and fire the gun).
Please note that a MP 40 is what is called an "open bolt" weapon. That means that you don't "chamber a round" in the conventional sense. The chamber is always empty. When you want to fire you make sure the bolt is pulled back (it's held there by spring tension) and not in the safety notch. When you pull the trigger the bolt is released. The bolt will fly forward, pick up a round from the magazine, load it in the chamber, and *instantly* fire that round. The gas from the bullet firing pushes the bolt back against the recoil spring tension. If he keeps the trigger pulled back the bolt will travel all the way to the rear and then, under spring tension, fly forward again to strip the second round from the magazine, load it into the chamber, and fire it. This will continue until he lets go of the trigger, which will stop the bolt in the rearward position. (Or until he runs out of ammo if he just holds the trigger down). When the gun stops firing the chamber is always empty. (The bolt fired the round in the chamber and then was caught to the rear by the sear when he let go of the trigger or the bolt slammed forward on an empty chamber if he ran out of ammo).
If you want him to use a rifle, give him a captured German K98. This bolt action rifle holds five rounds in the magazine. Let's say he has the five rounds loaded, but carries with an empty chamber. In that case here's the scenario:
He runs up into the balcony/choir loft when he sees the SS outside. He quickly loads the chamber by rotating the bolt handle up, pulling it to the rear (to chamber the round) and then pushing it forward and back down. This loads the first round. The safety is OFF.
The SS comes in. He aims at one, from the choir loft, and fires. A full power rifle round into the back will likely definitely kill or at least incapacitate a man. No need for a head shot or a heart shot.
He hits the first SS man and very quickly (he has practiced at some point) rotates the bolt up, pulls it to the rear (the empty shell comes out now) and than pushes it forward and rotates it down to load the second round. This takes maybe a couple seconds, if he's practiced. Now he's ready to shoot the second SS guy. The problem is, the SS guy would have time to yell for help, or take cover behind a bench, or the altar, or run back out of the church. He might not look UP right away, but he's not going to just stand there. He'll do SOMETHING.
Still, you could have the SS guy take cover behind something that would protect him from someone on ground level, because he doesn't know where the partisan is, and have the partisan shoot him because he has the elevation.
Personally, I'd give the partisan the MP 40, have him ready, and then have him fire a short burst into the first guy and quickly change targets to fire a short burst into the second guy, before either one can react. That's very realistic for a submachine gun and close fighting like is exactly what they were made for. It would definitely work better against two SS at short range than a bolt action rifle.
A burst of anywhere from 5 to 8 9mm pistol rounds right into the body would, again, be enough to realistically kill or incapaciate the Germans. No need for head shots, etc.
As to the noise, I disagree and think that having the SS using a machine gun for the exeuctions is plausible. If they want to shoot a lot of people that is the quickest way. He could fire the MP 40 while the machine gun fires, which would help with the noise. If it's a big stone church, that would help as well. Again, if you write it correctly, you could justify the SS outside either hearing or not hearing the noise, as needed.