Defense depends on who you are guarding. You can yell "weenie smallball" all you like, but as more and more teams are putting perimeter players at the 4, the utility of guys like JT wanes. Especially guys like JT that aren't great at punishing smaller players who guard them, nor at protecting the rim.
That's why I like Koufos. As you say, he's skilled, physical center, who can protect the rim when Cousins sits. If we're going to go big, I want to see us go BIG, with some Koufos and Boogie lineups, and see how the small teams try to get away with that. Then use Rudy at the 4 for certain stretches, in certain matchups (which I do think is more often than it may seem at first--I remember putting together a list before but the short answer is 'not everyone has a Z-Bo').
Yes, there's a concern about allocating resources when you already have JT and Landry, but "stretching" Landry is certainly an option (opening up $4 million in space by my math).
All of this, of course, assuming Cauley-Stein is off the board at 6. I'm assuming in that scenario we draft someone like Winslow who can help with the perimeter D. If WCS is there, though, I agree that changes your priorities--there's certainly not enough minutes for Cousins/Koufos/WCS and JT all to be happy.