As they said in Pirates of the Caribbean, its more of a guideline.
If it makes for more excitement to go to or drop out of warp in a system, then I say go for it. If it makes for a more exciting story to get into the scientific ramifications for doing so, I say do that as well.
If at some point in the future, we find that going to warp while inside a solar system is a bad thing, then I say we shouldn't do it. Makes sense, right?
I look at it as more of a speed limit thing. In the Star Trek universe, we interstellar travel we have to consider. Inside a solar system, where it's not unusual to have increased traffic, the speed limit should be lower. Thus, no warp inside the system.
But there are times when you have to gun it.