Right, so steam seems to hold a grudge against STO at the moment since the STO patcher and Steam dows not play along very well. So what I did was to move the game out of the reach of steam, and let the STO launcher do its thing.
EDIT: I do not take any responsibility if you break your computer by editing the wrong things in your registry!!
1: Exit steam completely, and make sure it does not run in the background.
2: Open up your windows explorer and navigate to your steamapps\common folder. (Mine is C:\Program Files (x86)\Steam\steamapps\common\)
3: Right click on the "star trek online" folder, and select "Cut"
4: Make a new folder somewhere (Mine is C:\Games\) and right click somewhere inside that folder and select "Paste".
5: Wait until the move is complete.
6: Open up the registry editor (Hit Win+r, and type in "regedit")
7: Navigate the registry to HKEY_CURRENT_USER\Software\Cryptic\Star Trek Online
8: Change the key named "InstallLocation" to wherever you moved the game to. (Mine is C:\Games\star trek online)
9: Go back to your windows explorer and run the STO launcher by clicking on "Star Trek Online.exe". Log on and the usual, and then it should proceed to download a relative small patch instead of the whole 10GB.
10: In the launcher click "Options" and check the checkbox named "Force verify" and click OK. It should then verify your files and redownload those that are corrupt.
11: Remove the game from your steam games list.
This should prevent steam and the STO launcher from having a battle about who have the latest version of the game. This worked for me, hope it works for you!
Why were you forced? Stop the patch process, copy the files from your old install to the new install folder, rerun patcher to fix any possibly corrupt files. Should take 15-20 minutes instead of hours redownloading the client.