If END { ... } blocks are not working, you are not properly cleaning up the Perl interpreter from your C code. See perlembed for how to clean up.

You cannot prevent a program from being traced or being run under strace. Maybe you want to read How can I hide the source for my Perl program?. In general it is very hard to hide the source code of a Perl program from somebody determined. There are approaches to make it harder, but no way to make it impossible.