No. However you will still encounter some distinct features of EB in RTW after installing EB on your PC. The reason is that not all elements which EB modded (such as vegetations, GUI) could be stored inside the mod's own file folder (RTW\EB); and have been placed inside the RTW folder instead.

It won't hurt game stability if you go about and play RTW Vanilla; but it is like "EB was here" has been written all over it: the loading bar for example will be green - not red.

This is precisely the reason why we recommend players to have multiple copies of RTW 1.5 installed: this way they can play both EB (on one copy) and other mods (on the other copy) without such side effects. It is not required per se: people have posted that they run EB just fine alongside other mods without ill-effects. (Which is the entire idea behind putting your mod inside a mod-folder: allowing the player to run multiple mods on the same copy of RTW.)