honestly the current rules are not that bad, especially when compaired to what they used to be in earlier editions, its one of the few things i like about the current edition.
as for how to handle it, so far i've read a lot of good ideas and of them, i would have to say that NPC hacker would probably be your best route, it keeps things flowing and allows you to wave teh group past problem spots that would have eaten up a lot of game time.
that said i really think that having a PC hacker is the best, and thats coming from someone who used to play a gunslinger adept and was stuck with a technomancer for his current game, i'm actually starting to like it