see the way that the linear alternator stroke is limited in the free piston Stirling engine on this link http://peswiki.com/index.php/Directory:InfiniaCorp where the linear system is not directly coupled with the cyclic power source of the solar Stirling engine. This technique is used in concentrating solar power systems that track the sun to convert thermal heat into electricity, but limiting the stroke of the linear movement.
it depends on what type of LA you are using. With our Moving coil type (light moving mass) there is non linearity in the suspension, so for large excursions efficiency drops and it is partly self limiting. There is a backup feature where the moving part hits rubber end stops.
Moving magnets have more energy stored in the moving part, so end springs with dampers may be a better, but more complex solution.
Electrically loading also helps. Depending on your thermo-acoustic system , you can stop oscillations with electrical load. We used a voltage limiter to restrict movement. It worked like a variable zener on the output. No current up to a certain voltage, then it took lots of current to keep the voltage (reasonably) fixed. One just needs to calibrate the set voltage limit for the max excursion required.
Hope this helps.
Get back to me with more detail if you still need help