it will be installed and enabled
Can we make it so that it would not be enabled by default? For instance, we wouldn't want favormod enabled 100% of the time as its a specialty game. We wouldn't even want uberfix or the enhanced ai mod enabled 100% of the time either. The reason is that folks without these mods won't be able to join games hosted by the folks with the mods enabled - and we won't have a 100% adoption rate using your launcher. I can get us a 100% adoption rate for anyone that participates in the upcoming tournaments, but that's about it.
Also, are you really sure that your program enables the mods by default? A quick test would be to disable whatever mod your are talking about in the mod manager. Then delete the mod. Then run your launcher and verify that it is now showing up as enabled in the mod manager.
If you actually have any flexibility, I'd say enable the enhanced ui mod by default and all other mods should be disabled by default.
I can test for you in windows 7 64.