There is two ways of reading 2d10 for percentile. It is possible to roll 100 both ways. Either way is perfectly fine, though you should definitely establish beforehand which way you are doing it.

One way is with the ones die being 1-10, with the tens die being 0-90. 0 on the tens and 0 on the ones would be 10. 9 on the tens, and 0 on the ones would be 100. Some people like this way of reading the dice because the ones die reads the same whether you are using it as a d10, or as part of a d100.

The other way is with the ones die being 0 to 9, and the tens die being 0 to 9. 100 would be 0 on the tens and 0 on the ones. All other numbers you simply read the dice as they are, 0 (tens) + 5(ones) is 5, 9(tens) + 3(ones) is 93, 4(tens) + 6(ones) is 46. People like this method because you simply read the dice, without adding. You could also have it be 0-99, though again, that would need to be established ahead of time.

Your friend interpreted the dice wrong, since in neither of those cases is a 0 and 1 a 100.

Just going with it is absolutely the right thing to do. In game, just go with it, and if it's something that's going to bother you in the future, bring it up with the GM after the game (in a friendly, non-attacking fashion). Also, Eclipse Phase is not an easy game to run, even for veteran GMs, so I'd give him even more slack than normal.

Make sure you talk to him about both the way to interpret % dice, and also about whether or not it's acceptable for you to be offing party members.

Side note: "Shoot-first-ask-questions-later" in Eclipse Phase? Really? In my Eclipse Phase campaigns, you better ask questions first, second, last, always, and if there are any shots fired, nobody had better even suspect you had a relationship with the shooter.