Ugh!

Well, for the rain, could you put a tarp over the rack? You could keep the tarp in your cube (someplace other cyclists could get it, labeled prominently "RETURN TO SALSAMTB!"). If you can get one with re-inforced holes, you can lock it to the rack, too.

You could also bring (sneak) your front tire (if it's quick release) into your cube to deter theft. Back in my day (1987), there was one student who always came to lectures with his front tire.

Maybe organize rides at lunch to show management there's a solid group of bikers at the company? And, er, hide you bike in a stair well with another cyclist, if there's enough room left for safety.

If you make friends with security, they might give you a wink and a nod when you bring your bike in during bad weather. (This is advice I should follow more myself -- attracting more flies with honey and all that.)