I have been on bcp since 18 (28 years) with a few years of not being on it. I have not noticed any increase in CD due to the pill. I can't discount that there could be a trigger relationship with the CD, but I can't testify to it being mine. I had CD symtpoms since i was a small child. I do notice that I always feel worse around my period and it being lighter on the pill has helped, but I also had a rupture that entangled one of my tubes so I seem to cramp every other month there any way.
As far as the clots, I was just tested for a chest clot, but it was a precaution. It turned out the inflammatory marker increase was just the kick off of my current big flare.
I also tried the depo shot and HATED it---it made me gain an enormous amount of weight, very emotional and I also quit as it supposedly took longer to get out of your system if you decided to have kids.
Hope this helps in your decision. Regardless of what you choose, it is great that both you and your doc are really looking at everything.