It’s easy for me to say with no time pressure and having had years to think it over, but I think rapidly decaying memory integrity would solve that issue. Saying a person’s data was large and complex and pushed even the limits of the technology would explain why they couldn’t just digitize everybody. The computer can only hold one pattern at a time and/or it degrades quickly.

This same caveat could also create limit on the amount and complexity of matter that could be transported, as well as create drama around technological arms races to build better computers to transport more crew at a time giving an edge to boarding parties to one side of a war.