"There’s a lot of projects, a lot of needs in the district, so there’s other priorities we have to put in place ahead of this,” Hopkins said. “This system is still running."
TFA doesn't give any particular timeline, but it sounds like they are betting on it running for a few more years.
As for the need to overhaul the system eventually, reasons might be something like: Scarcity of parts increasing, parts and labor for working on this crufty system being outside of their established maintenance and IT contracts (meaning extra delays and extra cost when something finally does break.) Going without heat for weeks while they find+hire someone who can debug assembly on an Amiga might not be acceptable. The computer system communicates with the hardware by RF - probably without any kind of encryption. The same frequency bands are used by maintenance walkie-talkies, and TFA mentions the maintenance guys having to work around that by "OK, Nobody use the radios for the next 15 minutes so that we don't interfere with the HVAC system." All this sounds pretty compelling to me.
My guess is that the $1.5m - $2m cost cited is for a complete overhaul of the district's climate systems, not just to replace the Amigas. If the rest of the system is as old as the computers, there's probably a lot that needs replacing. At that point, building a cathedral of cruft around an Amiga on life support will be the thing they have no compelling reason to do.
Our OS who art in CPU, UNIX be thy name. Thy programs run, thy syscalls done, In kernel as it is in user!