I would consider myself as a quite specialist of blender’s game engine.
…And I can tell you that splitting blender into two separates softwares
would be a pain for creating games. Specially for beginners, but also for specialists.
If it’s the interface’s layout that bug you, just create a “window setup” for blender games,
and a window setup for others thing. Myself I have 4 setups explicitly named :
1-Scripts
2-Model & Games
3-UV & IPO
4-Nodes
I tell you, the key is to have a good setup. Don’t just
get forced to use blender’s default setup 
Also, I don’t follow you in your believe that making the game engine external would
make anything else go faster into blender, for the coders skills I’ve gathered lately,
I can tell you that “the code that isn’t executed, Isn’t slowing anything”.
…by example, when you model something, the fact that blender can simulate
water absolutely do not affect your modelling speed… just like the fact that you’ll
be able to simulate your object into a blender game does not influence anything.
(xcept the way you’re modelling the thingy of course heheh)
For the incredible confusions that bring you this game engine into blender,
Come on. it’s only a single sub-button hidden into the “button window” sub window.
If that confuse you that much, man, you’re gonna get hell confused with blender hahhaahh.
Ho… and there’s also a shortcut “F4” that will also invoke the Game engine panel.
…but I don’t think you shall bother with that, it’s only gonna create more confusion hahahaha…
…my bad…
More seriously, I think you understand that it might not be such a good idea.
Blender is know to do everything. If you start to divise it, you’ll soon end up saying :
(I never do any fluid simulations, let’s cut that off too)
…and than nodes goes out as well
…etc
Blender handle quite brilliantly all these different personalities, if you really
want to mess with it’s code, don’t waste a second of your life trying to split blender.
Instead, do something creative and improve or create a new function for blender.
There’s so much to do.
Anywho,
Have a nice day folks. 