If you can't get it to work with a slow and steady control of thrust, consider a puller design. They tend to be a bit more stable. For the lower thrust approach, keep in mind that you can do your interplanetary transfer in multiple burns. For example, if a burn is going to take 15 minutes at 50% thrust (or whatever level works so that your craft doesn't wobble), you can do three five-minute burns, starting each two and a half minutes before the ejection angle point in your orbit. As long as your burns keep you in the sphere of influence of the body you are leaving from, you can do this. Note though, that if you raise your apoapsis really high, it can take so long for an orbit that your ejection angle will change.