Your problem is unlikely to be related to .NET framework. Only versions actively in use by an application are actually loaded into RAM. If you've got constant hard drive activity, something else is going on, such as a background virus scan, something auto-updating itself (like if you have Windows Update set to automatically download and install updates), or possibly a virus/malware/trojan using your computer as a torrent node, DDOS bot, or something along those lines.
The only negative effect of an "extra" version of .Net framework on your machine is the use of a few MB of disk space.