I've tried to analyze this issue a little but haven't got to the root cause. 
Judging from the backtrace, it seems like the following happens:
1) the main thread of jackd sends the cancel signal to the RT thread.
2) the RT thread starts unwinding (processing "catch" sections in code)
3) for some reason that I haven't figured out, std::terminate is called, which 
according to http://www.cplusplus.com/reference/std/exception/terminate/  is 
"Function automatically called when the exception handling process has to be 
abandoned for some circumstance that makes impossible to continue with it. The 
terminate handler by default simply calls abort."

In addition, the abort handler itself crashes due to bug 983835.

** Changed in: qjackctl (Ubuntu)
       Status: Confirmed => Triaged

** Package changed: qjackctl (Ubuntu) => jackd2 (Ubuntu)

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https://bugs.launchpad.net/bugs/956438

Title:
  qjackctl unable to stop jackd2

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