In many non-US keyboard layouts typing the ";" requires holding shift as well, so not sure how bad this issue is in actuality.
Most programmers I know use native+US layouts (like you), a minority always uses US (like me), almost nobody uses a native layout to code.
What I would do is this:
- Replace them with a single quote -> E' instead of È or É and so on.
- Ignore all uncommon marks.
In most contexts, it is perfectly acceptable to do that. A native speaker would understand without giving it a second thought or considering it impolite. I write emails to my boss like that.
If I had to make something meant for the public (say a UI, or a document), then I'd switch to the Italian layout for that purpose only and then go back to the US one.