I haven't really decided on a side yet, but started originally to go with the rebels after Helgen.

My main goal is to join the thieves guild and dark brotherhood, then start the whole dragon business or not. This is my third attempt to play the game in full, somehow every time there was something in between. The furthest I ever got with the dragon-quests is Whiterun and talking to the Greybeards, being member of the Thieves Guild and Dark Brotherhood but haven't finished decorating the hideouts or finish all the contracts.

Twice now I met some Imperial Soldiers on the road near Riverwood and Whiterun with a prisoner and since they were rude to me, I killed them and freed the Stormcloak prisoner. Will this affect my reputation, if I leave noone alive?

I remember in one attempt going with the Imperial Guards after Helgen and the soldiers were much friendlier in Whiterun.

I really enjoy it at the moment especially with timescale 5, as it is not as stressful any more with so many day/night cycles. Lots of mods like interesting NPC. Also the guards dialogue mod and wonder if this might be the reason they want me to pay a fine every time I get to Whiterun? The guards in Windhelm seem normal.

No, Skyrim does not have faction reputation so as long as you kill all witnesses, you should be fine.