Nah you should be fine. Having the whole lot balanced is great for making a high revving engine and is worth doing if you have the engine in bits. Just balancing the flywheel after it has been lightened is fine as it's better than not at all.
Having a balanced flywheel and the rest stock is not going to cause more damage than before unless it inspires you to go everywhere bouncing off the rev limiter and driving it like a complete loon which would kill any engine.
I've run a lightened and balanced flywheel on a mini without having the rest done and it was much smoother and picked up much quicker. I never had any undue wear on the rest of the bottom end as a result.
