Yeah, the whole "bowl at your own risk" idea has been around for a long time now. Hell, the center I grew up in had a sign that said "not responsible for damage to PLASTIC or "soft-shelled" bowling balls," so that approach isn't new.
Nevertheless, from experience, I've found that most owners will be decent about giving you satisfaction if you're a regular and you don't come at them like a d-bag when it happens. To be clear, I'm not saying you went at the guy at your center in the wrong way or anything; I'm simply saying that I've seen owners shut down and point right to the sign when Bowler X comes at them ball in hand ranting and raving about what the machine just did to their ball.
In the end, the decision of whether or not to leave the center is totally up to you. If you feel like the center let you down and has acted inappropriately, then that's probably your answer right there if you have other centers nearby to give your business to. On the other hand, if you've known these people for many years and have always bowled there, it may be worth having a conversation with them to tactfully explain your dissatisfaction with how they handled it. Maybe the guy apologizes and/or changes course. You never know.