Interesting. I don't think it would be appropriate for several of the reasons mentioned (possible breeding of animals unable to birth safely, expense, inability to reach the 'milk bar', etc). However, the study actually reads a little different than what has been said on here. While birth size and parameters were significantly affected, height at the withers after 3 years old and other parameters were only minimally affected as adults by the process. Seen as here:
However, both the reductions and the increases declined to only 5% at 3 years of age. This decrease in the disparity between body dimensions as the offspring approached 3 years of age was occasioned by either an increased ‘catch-up’ growth rate in the Tb-in-P animals, or a curbed rate in the P-in-Tb animals. However, this discrepancy in growth rates between groups did not occur in a continuous manner throughout the 3 years of measurement and monitoring. Although they remained smaller or larger than their respective controls during the study, significant differences in most parameters had disappeared by 6 months of age.
So, while technically true that you will see a difference throughout life...it is not a massive difference. At birth, yes, but then they begin to direct to their genetically pre determined size. Ironically, this same study has been used extensively in both my undergrad and vet school classes to point out that horses will end up pretty close to their genetic size, regardless of dam size (if not genetically related).
I would worry that the full size mare would drown the mini foal with milk if nothing else (assuming it could reach, which I suppose is possible, considering that birth size is heavily influenced by uterine size).
The unfortunate thing with using ET in minis is that assisted repro technologies are just NOT used by mini breeders. Rarely do you see anyone offering stallions for cooled/frozen semen, or AI'ing their mares, etc. If we won't do that (for many reasons, some good), then I think it is highly unlikely that ET would ever take off for minis, unlike many sporthorses/warmbloods.