If you're doubting the book because of things going on in life besides the writing -- stress, pressure, etc. are getting you down -- I'd say keep going. You may still have to revise substantially later, but there's no point in letting external considerations mess with your process.
If, on the other hand, you've legitimately seen a flaw in the plot and see a way to rework it, you may want to go ahead and begin revisions.
I had a similar experience on my second book. Although my plot essentially remained the same, the personality and motives of a significant antagonist changed dramatically once I got into the work. Although the antagonist's actions did not have to be altered, I realized that my main characters would have to have very different reactions in order for the story to make sense. I stopped (also around the 50K mark), went back and realigned everything, then got back on track.
Basically, if you really know what needs to be fixed, go fix it. If you're just unsure, I'd say keep going; even if you do have to edit later, sometimes perspective is better when you can see the book as a whole.