IMHO, it really boils down to what you want. Even if the value of the car were off by over $1000 at trade-in, the monetary amount is most likely small relative to your overall enjoyment of the car.
Here's my personal opinion. The sunroof is as hedonistic as options get, and it does compromise structural rigidity...but I drive my car on the streets 95% of the time, and I take my car to the track 5% of the time. That structural element would really only bother me at the track - the rest of the time, it won't bother me in very spirited street driving. That's why, during my car search, I decided not to care whether the car came with a sunroof.
But that's just my opinion. You seem pretty intent on leaving the sunroof out. My last car didn't have one, and to be honest with you I didn't miss it more than a couple of times a year...and those days, what I *really* wish I had was a roadster.