If I install the pre-release expansion will I still be able to play multi-player with people using the vanilla 2.0 game as long as I disable the expansion in the settings tab?
No, you won't be able to play with people on vanilla 2.0, but that's nothing to do with the expansion. Even non-expansion-related prereleases are not cross-compatible with differing versions of the game, because the simulations are different when balance changes are made, and so you'd run into desyncs if people don't have the same version as you. So, someone on 2.0 can't play with someone on 1.301 any more than someone on 2.001 can play with someone on 2.0, because of that desync issue.
On the bright side, if everyone in your group is interested in playing with the non-expansion prerelease features, they can all just install that (for free of course) and turn off the expansion, and then you're good to go. You'll all need to keep up to date on the same prerelease letter version to be compatible, though -- so if one of you updates, you'd all have to, again because of the desyncs issue. This is how we do our internal multiplayer testing, incidentally.
Additionally, you can easily "install" AI War in multiple folders on your computer, if you want to have a prerelease version and a 2.0 version. To make a second install, simple copy your existing AI War installation folder to a new location, and viola -- a new install! The game does not use any registry settings, so assuming that you have write access to the directory you created, the game will create a new settings.dat file in that folder, and you can have completely separate savegames, settings, and so forth there. So easy to have a separate "prelelease copy" of the game in addition to your vanilla "official version" copy of the game, if you are worried about compatibility in multiplayer games.
BTW me and the 20 or so friends I got to buy this game on steam are having a blast and are all totally addicted. The only thing in the game that annoys me is the star ships always end up on the outside of my fleet so they don't enhance many ships, maybe you could program them where they try to stay in the middle of the group where they would be most useful.
Glad you are enjoying the game so much! Thanks for your support of the game, and for spreading the word.
For Starships, they now have a higher collision priority, which should generally make them stay more near the center if you put them there. The CPU overhead for trying to add in more calculations beyond the recent collision priorities would drag down the rest of the simulation, unfortunately.