Thankfully the official ATP rules cover this eventuality:
" E. Ties. When two or more players have the same total number of points, ties shall be broken as follows:
1) the most total points from the Grand Slams, ATP World Tour Masters 1000 mandatory tournaments and Barclays ATP World Tour Finals main draws, and if still tied, then,
2) the fewest events played, counting all missed Grand Slams, ATP World Tour Masters 1000 tournaments they could have played (as described under A. above) as if played, and if still tied, then,
3) the highest number of points from one single tournament, then, if needed, the second highest, and so on."
Assuming that Murray reaches the final this week, and Federer and Murray match last year's performances at Rome next week, then by the first tiebreaker Murray has 6,480 points and Federer 6,370, I think, so Murray would just edge the second seeding (although I've only checked this in my head so could have messed things up, and they are close enough for me to have got things wrong!).