Acceptable to adjust colour levels dynamically I am using Premiere Pro CS6 to produce a short film and have some questions about the levels video effect.
Is it generally considered good practice to make adjustments to the RGB levels throughout a clip? For example, I have a single take clip where the scene changes drastically over a few seconds from an environment with heavy reds to an environment with heavy greens and blues. Trying to even out the scope at only 1 of these points means that I'm clipping the highlights at the other unless I make some changes. 

Obviously this is an extreme scenario but I'm thinking about perhaps scenes where a character walks across the shot wearing brightly coloured clothing that causes one or more channels to clip. Should you adjust the levels dynamically then or just set them so that they won't clip at the highest points so as to avoid strange color casts during that short period. Or should it even be more involved with something like rotoscoping to create a mask over the object and adjust that separately?

I know these are pretty loose examples but I'm just trying to avoid getting into bad practices if there's generally a right way to go about things like this.
What you're describing is color grading / color correction and yes, it's perfectly acceptable, almost mandatory for a good presentation. Usually it's done scene by scene, but it's not at all unusual to correct within a single shot, or even different areas within a shot.

To do it well you should explore a dedicated grading tool like DaVinci Resolve Lite.