Wood burning stove pipe through the ceiling and roof
Yes you will compromise the truss.

Each pipe supplier, if not, the stove supplier should have the allowable amount of elbows and the distance it can be offset with the elbows. Although I have only seen this with the insulated pipe behind walls and with additional supports. What you need may not look the best, but if it is allowed, it will keep your truss from failing should it be cut.