There are ways around this. One is that you can prevent automatic syncing of your iPad and iTunes when you connect; there are two boxes to check/uncheck. for the first, when the iPad is connected, go to the Apps tab and look for a box underneath the app list titled [something like] automatically install new apps. Make sure this box is UNchecked.
Then, in iTunes, go to Edit > Preferences > Devices and find the line "Prevent [iDevices] from syncing automatically" and make sure there IS a checkmark in it.
Now, every time you connect the iPad, you will be in control of syncing. To keep the iPad and iTunes in sync, I use the "transfer purchases" line to move all the apps over to iTunes and keep it updated. I do this "transfer purchases" every time I connect the iPad, just to make sure iTunes knows and has what I have on my iDevices.
With all that set up, if you want to delete all the apps from iTunes, then you can - and your iPad will not "lose" all your loaded apps. Just remember two things: (1) If what you have on your iPad is not in iTunes (and synced over), a good backup of your app data will not be made. iTunes, as an app management tool, will not have a clue what is on that iPad. (2) If you ever sync the iPad to iTunes, iTunes will remove all apps from your iPad that are not in iTunes - just as what is happening to you now. Again, iTunes is designed to be an iPad backup and management tool. It is designed to mirror your iPad.
Long story short (or ended): If you have an app on the iPad, please do keep it in iTunes on your computer. It will save you hassle and heartache down the road.
Marilyn