Wow! Freeworlds certainly has grown into the largest MOD size wise that I've seen.
270 ships? That's an incredible amount.
The most I've seen in a MOD is WTS-World which adds over 130.
You must have a lot of dedicated people working on the project.
As far as bypassing the Mod Manager goes that's fine. You can make an exe or zip file that extracts directly into the Freelancer folder.
If you want to try an install program check out the Clickteam website
http://www.clickteam.com/English/index.php go to the download page at
http://www.clickteam.com/English/ourdownloads.php they still offer a freeware version and an evaluation version of their Install Creator software.
Most likely there are files that get left behind when people are saying they are experiencing problems when deactivating the MOD.
DLL files are notorious for causing trouble.
I've even seen DLL files get left behind after deactivating the MOD, in other words they stay in the folder and that can cause trouble especially if you switch MOD's or upgrade to a different version of the same MOD.
That's why I say a lot in post that deleting the Freelancer folder before a reinstall is the best way to make sure you get a clean install.