Performance issues with Migrate Cron update
Updating all nodes every couple of minutes is bound to kill your performance. It's write-heavy and invalidates caches and there is no way around it in any possible CMS, not only Drupal.

If you cannot decide which nodes needs to be updated on XML read, try to decide on export, and export only nodes that changed since last time. Perform full export-import once a day, deep at night.

Other way around it is to write a custom module that would perofrm following steps:


Download XML file to local variable
Compare checksums of current and previous XML

If checksums was equal, exit.
If checksums was different, perform import. 

If changed update XML checksum.


That way you will only write anything if XML was changed - couple of times a day instead of every other minute.