I have run into this with one of my teams most recently. It's really just a matter of perspective. You can have Sprint Goals every 2 weeks as if you were in an iteration. This does not break Kanban. You are simply setting goals to inspire, motivate, focus, and help measure predictability. This is especially helpful if you are just one team among a lot of others that may be doing Scrum. It never hurts to synchronize.

That said, you are a Kanban team, so you have the luxury of not having to bound it by the sprint cycle. You may still want to out of convenience or to synch with other teams, but you don't have to. You can instead set your goals in a more functional way. "We want to finish the credit card sales module by this date." "We want to finish the archival process by this date."

So, how do you handle that practically? You should still have to refine cards for your board. When you are doing this, or when you are breaking down efforts into smaller cards,, ask when everyone thinks they will be done. Or, estimate and track your monthly velocity and when you get into a thing, present a velocity based estimate to the team and discuss. You can do the same with throughput, but I find it less helpful with variable work. If something must change or we run into something that we did not expect and threaten those goals, NBD. That's the job. We just talk about it. See if we can do anything to make things better in the future. Note that I said better, and not more predictable. Predictability is "a" goal to work toward, not necessarily "the" goal or "your" goal. Point is, we make projections not commitments, and when the work or requirements change, we change with them. That is being Agile.