If you ask me, the way protons, neutrons and electrons act in TPT doesn't even remotely resemble what they act in real life, even if TPT isn't about realism. So I suggest a few minor changes to the way they work.
I don't see many saves with protons, neutrons and electrons all at once and in close proximity, so I don't think many saves will be broken. Also, I'm not exactly sure how difficult this would be to program, but I don't think it's going to be that difficult.
Edit: Perhaps it could be an option, set off by default.
Many saves use protons, neutrons, and electrons together, for example lasers, fusion reactors, fusion bombs, etc.
Unfortunately, it's too late to change this, because it would break many saves. The electron/proton interactions you suggested could be programmed relatively easily (It would reuse most of the code from gravity simulation), but it would make the game slower, like gravity does.
Anyway, this idea would ok if there was an option to turn it on or off.