Like Fearia, I haven't seen a video, so my opinion is just in general, but a lot of it is very situational.
If, and only if, you were practically gassed and went for the takedown, then it would seem like a legitimate move to go for the sub off the back. Sure, clicking the stick is easy, but at the same time, if someone is gassed and about to get rocked, holding the left trigger and pushing forward on the right stick is just as easy to do as well to escape the stand-up. Another thing is it sounded like he tried it once and happened to get it. It would be a totally different story if he kept doing to over and over like Meaty did in the past.
As much as I hate saying it (NHL guys will know what I mean), it's in the game, so we have to adapt. If you (in general, not just Nate), are low on stamina, the best is to engage in the standing clinch (not the single collar clinch though) and grab on while your stamina regenerates. At that point, you run the risk of getting tripped/slammed/thrown, but you can't get knocked out or subbed from that position.
Again, these are just my two cents, and each side has a valid point, but also a valid counter-point.
Like I said earlier, it's in the game, but short of outright banning certain techniques, they next best thing is to learn to adapt it.
Edit: Serves me right to start typing a response, walk away, then finish- A vid gets posted in the mean time. I'll check out the video and update my view on the fight itself once I watch it.