Yeah, I have that and a little loading screen now, the game can be shut down freely, it just won't let you start a match until everything's pregenerated.
The loading version is only going to be for server though, if you want to play single player then you'll get the standard version. I've been told by plenty of hosts that even 2Mb is a large byond game for them to host. Which seems strange, but I may as well oblige them.
You can always just generate the states you'll need for the current match. If nobody has the "big" base, don't generate the states for it. Only generate those states when you're starting a match where someone's using that base.
You can also start some processing when the game starts up but put delays in there. Put sleep(world.tick_lag) after each state is generated (once you have a title screen and stuff it'll take some time after startup before people can be in a match). This way the CPU usage might be high but it won't be maxed out (so the game doesn't freeze and people close it because they think it's broken).