How did you calculate that it would be more expensive? I was in the same situation as you. Actually I needed to train to about level 96, too. The stats were about the same, although my defence was a little higher (about 50). Here's how I see it, let's say you want to train your pet to Level 100 with 200 in other stats:
Start over
Level 0 to level 20 (leveling everything: Level, Strength, Defence and Endurance) will cost (2700*140) 378k (at the Academy 1DC and 2DC are about the same now)
Level 20 to level 40 will cost (7000*140) 1M (also Academy, 5DC)
Level 40 to level 100 will cost 7M (took this from
SpireMK's analysis)
Total: about 8.4M
Train from here
Level up to 100 costs 1.2M (20*2700, 20*7000 at Academy, 200*5000 total codestones [40*3*5000 and 20*4*5000])
Train Strength up to 200 2M
Train Defence up to 200 4M
Endurance is already nearly maxed out
Total: about 7.2M
There's not a real big difference in the prices, although training from this point onward seems a little cheaper. More importantly, is the current pet you have worth keeping? I wanted to keep my pet name, no matter if it were more expensive to train