I believe that he latest version of GroovyMAME does what you want...
http://forum.arcadecontrols.com/index.php/topic,135823.0.html
Quote:
- Cleanstretch feature (improved): now the -cleanstretch option admits these values: * 0 (in mame.ini) = auto, this value allows GroovyMAME to decide whether to use integer scaling. * 0 (in specific .ini or command line) = force fractional scaling. * 1 = force integer scaling in both axis. * 2 = fractional scaling for x-axis, integer scaling for y-axis. This option is manual only (can't be selected automatically). As suggested by Cools.
GroovyMAME support forum on BYOAC
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