You can overcome this if you remake your framework and include all needed
controller and view files as constants in each script to be executed, not
inside any block or function. But this kind of contradicts the idea behind
such frameworks.
If you opt not to encode PHP files, they are still protected but to lesser
degree than when they are encoded, and in theory they can get the source
of your scripts. When they are encoded, a hacker can't get the source of
PHP files in principle, all they can possibly get is those serialized
opcodes.