Technically, the Dalai Lama and TGIE have already "clamped down" as much as is possible on Serpom and Shar Gaden. I believe they do not receive ANY welfare or financial help anymore from the TGIE. They are completely cut off from the Tibetan community in exile. If I'm not mistaken, they also are no longer permitted to hold Tibetan passes (the yellow card) and may have to be Indian nationals.
Legally, I believe the Dalai Lama / TGIE have no jurisdiction over the opening of these monasteries. There is freedom of religion in India so as long as they are on Indian land, those monasteries would be allowed to exist; the TGIE have no right or say to close it down.
So I believe that these two very brave monasteries are functioning as completely independent monastic institutions now, the are beyond the governing laws of the TGIE.
Then again, perhaps this is also a part of the Dalai Lama's foresight - when set so completely away and separate from the TGIE, they are "forced" to develop new methods, new ways and not be bogged down by the old politics and restrictions of this old, archaic government. Surely the DL knows how backwards this TGIE is! It is compassionate of him, perhaps, to "force" them out - by doing so, they have only become even larger, more prominent than ever, and growing very, very, very fast.