Even when stacking missions I find it is easy to avoid the interdictions - just keep an eye on your scanner. Though admittedly there are still the odd ones where an NPC magically appears behind you without any prior warning... Usually I don't avoid the interdictions, though, as my combat score rank is the only one I need to work on.
I also find that if you go fast enough, those NPC pirates (or bounty hunters, depending what you are doing) won't catch up with you anyway. Or they only catch up just as you arrive back at the mission giving port to claim your money - that happens quite regularly, and always makes me chuckle.