Here's some shots from 3.2.2a in Noggit:
This is where the original entrance was:
The original entrance is still at about the same position, just below the map:
And here's a shot of the WMO of naxx floating above the instanced EPL:
Now, as for a reason to keep the instanced version in EPL:
For Kel'Thuzad's room, there's a bit of world geometry, that was made to look like northrend (snow and trees). This bit is still in use in the current instance. I reckon that it was easier for Blizz to leave the instance and its specific world-geometry in the original instanced EPL than to move it to a new instance. What is interesting, is that if you were to overlay naxx's WMO and Kel'Thuzad's world geometry, Naxx would engulf the remains of Stratholme, while KT's boss room would be In the unused section of EPL, above where the DK's start now.