Because it seems that I've encountered quite a number of buggers who will always interrupt me, no matter which merc I use. Whether it's Ivan or Magic, the 2 fastest mercs in my team, these enemies will always interrupt me whenever I:
a) shoot them
b) walk in their line of sight
c) noise alert them to my presence
How is interruption handled in the game? Does anyone have any ideas on how to take down these guys without getting shot at?

Hmm. is this question serious? Interrupt is part of game mechanics, although we do not really know when the game enables them, but it does happen. I don't think it is tied to any stat of any mercs. Also, the game gives US a lot of interrupts aswell, when we can use 1/2/3 mercs in the opponent's turn (depending on the situation)

In the first JA they seem to occur when a character has spare Action Points when ending his/her turn and sees a new enemy enter his line of sight. It might act the same in the sequel.