Hi Yulian,
there is no option for disable interrupts while single stepping in debugger options. The only way is to disable EE bit directly in MSR register.
But from my point of view, your problem is following (please correct me, if I am wrong). You have PIT timer which generates some time period and then interrupt is called. So before you are able to single step code in the interrupt, another interrupt is occurs. This causes, you are still in the interrupt handler. If this is your issue, there is simple solution. You can set freeze bit in PIT MCR register. This cases, that timer is stopped in debug mode.
Please let me know, if this solution is suitable for you.
Regards,
Martin