To be honest, the proper(TM) fix for that would be for apt to run at nice level of 15. 15 means the lowest possible priority, and 0 is the default priority for applications, thus all other tasks would have priority over apt and it shouldn't bring the system to its knees. You don't need a different scheduler for that.

Of course, it was a hindsight on Nokia's part not to make apt run at nice lvl 15 all the time. One way to get around that would be to simply rename the apt binary to something else and replace it with a script that calls the actual binary but with a proper nice level.