The eras are just so different. Whereas there used to be a tradeoff between speed and size, that no longer exists. Conditioning and nutrition are light-years ahead of just 20 years ago. Rules change, most notably what constitutes ineligible receiver downfield and pass interference.
A Wallace Wade team (1925?) gave up 13 points all year. The 1961 defense gave up, what, 25?
1992 gave up more points, but would have curb-stomped either 1925 or 1961. All of Saban's defenses from 2008 on would have run circles around all of their predecessors, including 1992.
To get a real answer, you'd need to measure each year's defense against its peers that year (or, say, a minimum of 2 years either way).
Measure Bryant's defenses from 1961-66 and 1971-79 against both national averages and ordinal performance. Same thing for Stallings from 1990-94, and Saban from 2008 to present. I'm guessing Alabama will stack up well.
But even that doesn't tell the full story. Measure the difference between Alabama and the next best competitor. Is the gap close, or is it tail lights at midnight in western Kansas?
Point of all this being: the true measure of the best defense is the difference between it and the next best alternative, as measured by the rules and other factors as they existed at the time.