Is it possible to pause the program when it runs?
I use VirtualBox (for StellarCracker). It probably reduces performance a bit, but allows me to Pause the entire VM when needed. Alternatively, I can adjust the VM's Processor Execution Cap to a lower percentage when needed.
But that's for next time, it won't help you now.
The only thing I can do is to turn off a couple of cores in Task Manager to make the computer respond again, but the program still lags
Can you adjust the priority? "Idle" seems perfect for cracking.