Would that make a difference? Killing is killing.
Well, the difference would be that in Barnabas' personal timeline Sarah has already told him that she'll never appear to him until he's good. And, obviously, killing someone isn't good.
but since he wasn't doing harm before that
As for not doing harm, I suppose that all depends on the degrees of harm one is considering. True, Barn hadn't killed anyone up to that point. But he had attacked Sandor, Charity, Beth and Dirk (which in turn had enabled Dirk to cause all sorts of havoc along with the death of Pansy and the extremely tragic death of Rachel), he'd forced Sandor to do things against his will, and he all too often treated Magda like she was some slave who was simply there to do his bidding - and whenever she balked, he'd threaten to kill Sandor. Not exactly the behavior of a sweet and lovable Mr. Nice Guy.