Allow me to answer this by providing a counter-example.
I own two iOS devices; An iPhone 4 and an iPad (original). I use slightly different application sets on them. For example I don't have a notification app called Prowl on my iPad because it's intended use is to get my attention anywhere I am. And the iPhone is always by my side or at least in very close proximity.
And of course, there are iPad only apps such as the iWork series until recently. Even then, I only have the iWork apps on my iPad because working on something like that on an iPhone is admittedly kind of terrible.
So, when managing my apps, if deleting an app on device deleted it in iTunes, the other device would lose the app on next sync. This is not a good thing for me.
When you delete an app in iTunes, it unchecks it from the sync list. This way you continue to receive updates for it via iTunes, and if you ever want the app back, it's a simple operation to check the box.
I do believe @Hand-E-Food's example of a paid app is a good example. While we know that you can re-download any app not in your library you already paid for, not having to jump through the "Yes I do want to re-download this app I purchased" hoops is handy.
If you deleted an app because of crashes or general instability, than you can watch iTunes and wait for it to update, and then update it and see if it's better.
Why is best answered by Apple themselves, as it was obviously a design consideration that I'm not sure anyone else here will have the answer too.
But unfortunately I don't believe you can change it. The easiest way to change it would be to delete apps only via iTunes, and not on your iPhone directly.
Yes - just delete the apps from your Library on iTunes and they won't show in the list of apps that could be synced.
The long version is click on Apps in the Library, then select one or more apps and press the delete key. Answer a few dialog questions to confirm you want to delete and move the file to trash (or not) and you are done. The next sync will remove that app from your iOS devices.
Do note, that if you don't sync for a while, the iTunes could see the apps on the device as new and needing a transfer back to your library, so be sure to sync sooner or just pay attention when a "items were found on your device" dialog pops up and asks you to transfer purchases back to the library.
Best Answer
Followed @lax solution: clicked the iTunes Apps tab (not in the "iPhone" tab!) there I could select and delete the apps.