Linux - Isolate process without containers

I have not read anything in the description of your problem that would prevent you from creating different user accounts for the applications. You can then use trivial file permissions for preventing interference:

chown app1 /var/lib/myapps/app1
chmod 700 /var/lib/myapps/app1
sudo -u app1 /var/lib/myapps/app1/run.sh

edit

If the evaluator is running as root then it can simply start the applications via sudo.

If the evaluator does not run as root then the applications it calls (in the normal way) can be installed with the SUID bit (set user ID) so that the process will run as the user which owns the binary file and not as the user of the evaluator process.

Depending on your distribution and kernel, you can use AppArmor or SELinux to contain your applications. Overall I'd say AppArmor is more convenient to set up and maintain. Ubuntu wiki has some articles explaining basic concepts.