Quote from UESPwiki:
This quest uses the Radiant Quest System to randomly generate a target location and waypoint for the objectives. In some cases the waypoint will lead to a random spot adjacent to the designated quest location. This is caused when the player has previously killed the Silverhand leader. Currently only PC users can fix this using console commands. This happens quite frequently at Valtheim Towers
I recently started a new game on patch 1.4 (original playthrough only had minor issues but i moved the save to a memory unit just incase i wanted to continue with it) and one of the first bounty quest's sent me to Valtheim tower's which i have cleared out, also started the Companions questline a few hour's after that so i am not that far into said questline yet but your post is a little worrying! another strange thing is the bodies have been cleared, i am not sure if the 30 day timer has been altered but i went past this location 4-5 days in game after i cleared it (on my way to Ivarstead for main quest) and there are no corpse's whatsoever!
Anyhoo i have been using UESPwiki for prevention/workaround's, for example after finishing proving honour with Farkas, you have to do another radiant quest before 'unlocking' the next main quest in that questline so naturally i saved before speaking to anyone, got my quest but looked up the location it take's place just to see if any other possible quest's (non-radiant of course) take place in that location, it did so i simply reloaded and asked the same person again which switched the location to one that does not have any other quest's tied to it.
I have to admit this way is a minor spoiler but i guess it's the best way to avoid any problematic bugs :/