Yes, but for two huge reasons:
1 - Deion earned the come-up through a ridiculously successful effort
Eddie George is another ex-NFL star who went to coach an HBCU. His overall record in two years is 9-13. Sanders went 15-5 his first two years (27-5 overall). (Both their schools were ~.300 the year before each arrived)
Deion won on the field. Deion reinvested HEAVILY in his school and community. Deion brought massive attention to JSU and, of course, himself. George hasn't won, and if George has reinvested heavily in his school and community, we the general public have no idea. And all that hype isn't an accident, it takes intelligence and skill, and it actually does matter a hell of a lot. I guarantee you that TState's players would like all the attention and money coming to JSU's kids.
And George is in Nashville. Just imagine Primetime Neon Deion selling Nashville. At Titans games and such.
2 - His ceiling is way higher than JSU's (or any other HBCU's) in relative terms
There is only so high any HBCU is going to climb, no matter who the coach is or how many times they win the SWAC (or OVC in George's case). Looking at it from the outside (in racial and demographic terms) I don't see what else Sanders could have accomplished for JSU/HBCUs. Him leaving sucks specifically because he did so much.
Overall, I would love for JSU to stay on the best possible terms with him, because it's best for them. Keep the train rolling as much as possible.