Hi,
if the differences in travel are small it will not overload or damage the guides as every real machine - especially most DIY machines - are more than flexible enough to compensate for this. If you can also live with the error in terms of abolute position tolerances it should be fine.
If the differences are large or at least larger than your precision expectations I think you have no other realistic choice than to get a pair of reasonable precise ones. Ball screw and acme thread spindles are available in different tolerance grades and most companies should be able to pick a well matching pair for you - even though this will cost a bit if your requirements are very high.
I know no control software that does travel mapping for 2 axis and then controls them independently to keep them perfectly synchronous. I've seen this only once for a single axis but don't remember where.
Closed Loop control of axis position is another option - but is is very expensive and only used for commercial high precision machines.
Christian
My CAM Software and CNC Controller: www.estlcam.com