Hello,
I already had that kind of situation with a server that have a high use of squid, lot of internet traffic.
Squid take long time to shutdown when lot of use.
Here is how I solve the problem, on command line I try :
service squid stop
and after check to see if it is shutdown :
pidof squid
If it's not stop, then I retry to stop it.
I retry until squid stop correctly.
When it's stop correctly, then you can start it again.
Hope this can help you.
Regards.