Hmm. It works for me using GMail as a test. (Yes its possible to set up a GMail account under Corporate Sync)
Using the default three emails as test subjects (the ones that Google always sends you welcoming you to a new GMail account) I was able to delete one of them on the phone, and after a manual sync/fetch refresh I logged in on my computer, checked the account and sure enough the file was deleted and wasn't even in the trash. It was gone.
The only thing I did differently, was from the Corp Sync screen, hit the menu softkey button, choose 'Email Settings', then select 'Email Delivery', then 'Fetch Schedule' and changed it from the default of 15 minutes to 'manual'
Seems to work fine for me. If I delete an email and hit the little refresh symbol on the top right, it manually syncs and within 30 seconds the actual email has been obliterated from the account when I check via my PC login.