Hmm... Do the 40k rulebooks have rules for the players getting infected? Now, for novices, you'd probably have to just kill the character, but if someone's a good enough role-player... Could make for an interesting story...
Creatures Anathema for Dark Heresy has the Genestealer, and I believe it also has rules for infection. It's not pleasant, and as far as I remember, almost certain death or turning, whichever it actually does to you.

And Deuterio12, I believe you confuse the Imperium of the 41. millenium with the Imperium of the time the Emperor was actually around, or at least treat them as the same entity. Both were radically different.