I agree that there are plusses and minuses of having footcups. However, I think that the benefits of them outwiegh the risks.
We use them in all compartments of our rafts (hyside 13'). Over the last eleven seasons have not witness any injuries caused by them. They do a great job of helping the guests stay in the boat on some of the runs we do where a swim could be less than desired ( Pine Creek, Gore Canyon). Of course, proper instruction by the guide on how to sit in the boat and how to paddle and where and when to "lean in" also help folks stay in the raft.
To say that they cause injuries is unfair. In my experience at other operations, when a raft doesn't have footcups, people tend to jam their whole foot under the thwart or in the gutter along the floor, even the lacing in the bow. This can sometimes be much riskier than using a footcup.
Just my opinion based on experience.