I flew out of ELP a dozen or so times while I lived there post-9/11, from Sept to Jan. FWIW, check in lines and security lines were never that long-- after a few flights, ELP regulars can attest that 45 min. to check in and clear security is usually still fine.
That said....
I don't agree with AA using all 5 agents to check in people for the ORD flight. I'm curious if people behind you ended up actually missing the DFW flight because of it.
My perspective, though, is to have a latecomers line, in the unfortunate event that someone is late beyond their control. Sure people will abuse it: people abuse the express line at the grocery store; people abuse handicapped parking spots and special seat designations at the front of buses. But by and large, it provides a courtesy in people's time of need, and it causes minimal inconvenience for the general populous: if 1 agent were checking in ORD, then your wait in line may have been 7 minutes instead of 5.