I'm really only old enough to remember the end of Mark Eaton's career, and by that time he was in his mid 30's and just a lumbering big who mostly took up space. When I've seen highlights of his early career it really surprised me how quick and agile he looked. He played and thrived in the early 80's era of the Jazz which was very fast paced. Mark started his career at age 26, so we only had 3-4 years of prime Mark Eaton and in those years he was a truly dominant defensive force, averaging 4.3, 5.6, 4.6, and 4.1 blocks per game (Rudy's highest is 2.6). His advanced defensive stats were pretty ridiculous as well with 6 seasons with a DBPM over 3 (Rudy's highest DBPM was 2.8). Mark's total defensive win shares are 48.0 vs Rudy's 41.5. I think there is a decent argument to be made that Mark was a better defensive player than Rudy, although I prefer what Cy said in that they were both perfectly suited for their eras.
Offensively it's not even close. Mark Eaton was a huge liability on offense, whereas Rudy was a great offensive player despite the hate. As big as Mark Eaton was he had a career fg% of 45.8% compared to Rudy's 65.4%. Rudy has a total offensive win shares of 52.9 compared to Mark's -3.2.