But he knew he'd be a vampire in 1897... I'm guessing he did. If he hadn't made that difficult choice the series wouldn't be the interesting thing that it is, but he had to know he'd end up killing people.
It might be nice to think Barnabas would be willing to make that choice, but the fact is that when he threw the I Ching wands in 1969, Barnabas had no clue whatsoever that he would travel back in time to 1897. He simply hoped to be able to communicate with Quentin's ghost. And he was horrified when he saw his changed coffin beyond the door and ended up inside it. He most certainly never suspected much less was willing to let that happen. But once he was in the I Ching trance, apparently there was no going back.
On the other hand, yes, he did know he would be a vampire in 1840. But he was already a vampire in 1970, so the whole vampire issue was completely moot.