The main difference ist that /usr/bin/perl is a fixed path to one perl (which is usually the one that ships with your operating system), while /usr/bin/env perl will take the first perl in $PATH.
I know it is OT, but ... does /usr/bin/env perl makes much sense at all? In this case, I could simply write perl. I feel that env is mainly useful when used together with options, such as env -i for providing an empty environment for a command...
You are right that /usr/bin/env perl and perl will behave the same way on the command line. However, as JavaFan points out below, they are quite different when used on the shebang line (since the former will look for perl in your path, while the latter won't).