How can I compare rates of evolution for two sets of proteins?
If protein alignments are sufficient for you, I suggest that you look at the eggNOG database. There you can download mappings from proteins to protein families, and for the families you can also download pre-computed multiple (protein) sequence alignments. 

I guess depending on the type of analysis you want to do you would have to trim the alignments to get only homologous regions (for example, see this recent paper[1]).




Wu M, Chatterji S, Eisen JA. 2012. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288, doi:10.1371/journal.pone.0030288.