It's fine to put a 3 gal batch in a 5 gallon keg. You might want to look into liquid purging the keg and doing closed transfer from fermenter to keg. It takes a lot of purges to get the O2 level where it needs to be to minimize oxidation (see the chart and table below) if the headspace starts out as air. The larger the headspace, the more CO2 is used to do an effective purge. Personally I liquid purge, closed transfer, and still do ~5X purges @ 30 psi.