can the quest mess up the ability to buy herjim?
It did, but at least that bit got fixed with patch 1.04.
I've just started this quest - took me quite a while to figure out how to trigger the actual events, after I had heard the rumours in Windhelm - but when I read that it has many bugs, I decided to follow the walkthrough (+ notes & bugs section!) of the wiki:
http://www.uesp.net/wiki/Skyrim:Blood_on_the_Ice
One warning that may or may not still be relevant....I'd go for sure, and take note of it anyway :
* When you are told to question the witnesses, stay away from Hjerim. Approaching the front door will trigger the 'Gain access to Hjerim' and clear the graveyard. This will leave you with no witnesses or map markers for the remainder of the quest.