I was looking at totals, not per-game averages. From each team's website:
Allen - 921 minutes, 176 assists, 74 turnovers (2.38 A/TO)
Canada - 984 minutes, 174 assists, 88 turnovers (1.98 A/TO)
Buss - 1163 minutes, 134 assists, 112 turnovers (1.19 A/TO)
I do tend think that (for point guards specifically) efficiency and passing should count for more than scoring. So yes, Johnson is ahead of Allen statistically by my criteria.
Side note: I suspect Baylor's official scorer is exceedingly generous. 674 assists in 32 games for Baylor compared with 552 in 31 games for ND doesn't make sense to me. It doesn't change this discussion, though, because you can lop off 80 assists and Johnson's A/TO numbers are still excellent.