Its your table, you can do as you please :p
Just be aware, there are some differences between DnD and Shadowrun (if you've never played before)...
XP (Karma) is awarded on a Per mission basis, and not per encounter in DnD..
So, while in DnD, the adventure might be to clear a cave infested with monsters, and the players earn XP for every monster they clear...
In Shadowrun, the adventure might be to get the Prototype Commlink... And that is what the reward is for, it doesn't matter if they defeat 1 or 100 security guards... the reward is the same. (generally 1 to 3 karma)
Page 269 of the SR4a has the write up for Karma and how its rewarded...
While every edition has its strengths and weaknesses, for me I feel 4e weakness was in overall character growth, as character quickly "maxed out" what they 'wanted' to spend karma on, and were forced to settle on 'optional' choices. So speeding up karma rewards just makes the issue worse.
Of course, that is only my opinion on the matter.