Somewhat bad at the beginning does that turn off readers? Just for example he is forced to do horrid things for the sake of keeping his own and others lives. Yet he understands that it is wrong and tries to fix his wrongs? When the character is forced to the dark side, yet is escaping their sins. What are your opinions on that aspect?
There are a few ways to approach the answer(s) to this question.
The published book: If we're talking about a novel that is published, most likely your readers will already go into the book knowing your main character has some redeeming qualities. (Thanks to the back of the book blurb, for example.) You can probably hold out a bit longer, because the fact alone this guy is boasted as the main character (ie: protagonist) suggests there's something good in him.
The manuscript: Before you publish, you've got to get past some readers, though. Beta readers, if you have them. Agents, editors. But the key here is just to show that moral side where possible, as early as possible. Antiheroes are some of the most memorable characters in fiction: Batman, Holden Caufield, Lucifer (Paradise Lost), Raskolnikov, Scarlet O'Hara, Han Solo, Severus Snape, Jack Sparrow, Jack Bauer, House, etc.
Consider, also, how other characters react to your main character. This might all depend on the POV for your novel. If your POV is your main character, then you might have to work a bit more to effectively show off his internal struggle. But if the POV is his wife, for example, then you might have a more obvious showcase for his good side right away.
Personally, I usually like antiheroes more than the hero-heroes. Try picking up a copy of Bullies, Bastards and Bitches by Jessia Morell if you're interested in the whole dark hero/antihero/hero/villain distinction.
Moral struggles can be very interesting. I'd be totally fine with it.
