There's nothing stopping you from removing QuickTime from starting at startup. You can delete its startup entry in the Windows registry.

All of the programs that automatically run at startup show up under one of three places:

1. Registry: HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
2. Registry: HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
3. Startup folder in Start menu

QuickTime's entry is under the first.