I have been staying away from the main story line and doing odd Misc quests and roaming alot. I took yesterday and started in on some quest clean up. Normally I will persuade or move along waiting for a new opportunity. I like that kind of character. I basically started killing everything. I was stealing and bashing in everyone. It did not make a difference if a hired hand at Black Briar or a guard at Northwatch. Will this affect my character going forward as to opportunities the game provides me?

It very well can.