Doing a quick check on 2.4 ini_set is called roughly a dozen times. Do a global search on your project, you should be able to get away with using SS since most of the references to it are in tests or functions which aren't critical.
ini_set() is used for example, to increase the PHP memory limit for SilverStripe.
I'd try re-enable this function if you can, there's bound to be a lot of places in the code that relies on it being enabled. You could get away with scouring the code base to remove these ini_set(), but I can't guarantee it's going to work properly on your server if you do.
Having exec() disabled is also probably going to cause you problems, as there's a few places it's used in the code as well.