The first ABS systems were actually mechanical not electrical, so not all ABS is "brake by wire" either.
Aside from that, it all has to be done through the centralised ECU so in theory it would be difficult for a team to abuse what brake by wire is for. We don't have traction control in F1 for example, and apart from the dubious rumours regarding Red Bull last year there have been no issues with teams trying to get around the regulations. I don't see why brake by wire is any different. It isn't and won't be ABS.
Aside from that, it all has to be done through the centralised ECU so in theory it would be difficult for a team to abuse what brake by wire is for. We don't have traction control in F1 for example, and apart from the dubious rumours regarding Red Bull last year there have been no issues with teams trying to get around the regulations. I don't see why brake by wire is any different. It isn't and won't be ABS.