Does cornstarch affect the pH of what I'm cooking?
I don't have any info on the affect of pH, but cornstarch can make your compote separate when canned: http://www.sbcanning.com/2011/08/canning-pie-filling-education-in-clear.html.

Two alternative thickeners are tapioca and clearjel.  I've used clearjel for canning with excellent results.  I haven't used tapioca to can, but do prefer it in my pies.

(posted as an answer per Sobachatina's recommendation)