I play skyrim on PC, and like many people, I wasn't able to trigger the dead body scene for "blood on the ice" to even start the quest. However, after doing some research on the internet, I learnt of a console command that allowed the dead body scene to take place:

setstage MS11 1

When I entered this console command, by the gods, it actually worked! However, I'm just not quite sure what repercussions this may have for my game, and I just want to be sure it's safe to do this before I proceed with the quest.

So, will this have any negative effects on my game in the long run? And is it safe to do this?

Since you're on PC the process will be much easier. You should be fine. Remember to break into the house if you start to have trouble.

More likely the scene occurred, but you were unaware and did not witness it?
I've played that quest numerous times and it always goes flawlessly...
Are you running the Unofficial patches?
Hope the setstage thing works for you.