I have done it via Sip Trunk also. For the most part it worked like a charm, however we did have problems with Find Me and External assignment working through the SIP trunk (Cisco used the real trunks, ShoreTel just has SIP running from SHoreTel). I have not been able to test it again for a couple of years but I think ShoreTel has opened things up to be able to sue Fine Me and External assignment over SIP. If you use a T1 interface between the Cisco and ShoreTel you would have 0 issues.
The only horror stories I had was the fact that both Cisco and ShoreTel told e it could not be done at the time, and neither would provide any support, but if you have a good ShoreTel person and a good Cisco router person (who knows SIP configuration) you will get through it in a couple days.