Some good points in here but I feel like you didn't quite get the critique. The comp pick component is an acknowledgement that due to Josh's increasing cap hit we aren't going to be able to pay everyone, and so like it or not there will be home grown players like Brown (or Rousseau or Bernard or Benford, etc.) who we have to let walk in the coming years.
Through that lens, is Brown the right guy to pay? I'd say there are legitimate reasons to think no considering his injury history and where he currently sits in our roster talent pecking order.
If we did let Brown walk, we'd be replacing him with a B- calibre player in FA or using our 1st or Minn pick not the comp pick which would presumably be BPA. It'd undoubtedly make us worse for a year in that spot, but none of these decisions get made in a vacuum - there are opportunity costs each time we do anything due to cap and pick scarcity.
I also say this acknowledging that at this time we have no details on the extension, and so any criticism is clearly premature. I will also add that it's possible Brown is turning into a valuable team leader behind the scenes, and so politically there may be motivations we don't see as fans. It's an interesting decision though.