1) First, it should be made perfectly clear that it is forbidden to "commandeer" a Sukah. This is stated clearly in Shulchan Aruch. The whole discussion here is if somebody wrongly did this, did he nevertheless thereby fulfill the Mitzvah b'Di'eved.

2) The fact that the Sukah is considered as borrowed actually works in favor of the owner because it means that the thief did not legally acquire the Sukah by seizing it. Therefore, the owner can certainly eject the intruder from the Sukah.

3) We may gain a little more understanding if we note that the Mishnah Berurah (OC 637:9) writes that it is actually permitted to walk into somebody else's Sukah without his knowledge and sit in the Sukah, as long as one does this in a way that does not disturb the owner. This is because there is a principle that a person is happy to have a Mitzvah done with his property. Similarly, there is a Halachah that one may take one's friend's Talis (on an occasional basis) without his permission because we assume that a person is happy that a Mitzvah is being performed with his property. However, if the Talis was folded, one must return it with the same folds and one may not take it out its place.

4) Similarly, concerning the Sukah, we may suggest that even though it was forbidden for the thief to commandeer the Sukah, nevertheless if he did so he fulfilled the Mitzvah because he did a Mitzvah with somebody else's property and that property never actually left the possession of the real owner, which is why it is considered as borrowed.

5) As to why the principle of "Mitzvah ha'Ba'ah ba'Aveirah" (a Mitzvah that comes by way of transgress) does not apply in this case, there are different opinions among the commentators:

(a) Rav Yosef Shalom Elyashiv zt'l asks your question (in He'oros b'Maseches Sukah, 31a, DH v'Rabanan), and he answers that not every transgression renders the Mitzvah into an invalid Mitzvah ha'Ba'ah b'Aveirah. Rather, it is only when the object with which one does the Mitzvah is an object acquired via a transgression that the Mitzvah is rendered invalid, even b'Di'eved. Therefore, if one steals an Esrog in order to fulfill the Mitzvah of Arba'as ha'Minim, his Mitzvah is invalid because it is a Mitzvah ha'Ba'ah b'Aveirah since the Esrog was obtained through theft. In contrast, it is impossible Halachically to steal a Sukah; land (or a structure attached to land) cannot be stolen because land always remains in the possession of the real owner. Hence, the Sukah is not an object on which a transgression has been performed because the Sukah itself was not acquired through theft.

(b) Ha'Me'or ha'Katan (a commentary on the Rif, printed in the back of the Gemara, page 14b of the pages of the Rif) writes that we learn from the Gemara here the Halachic conclusion regarding the question of Mitzvah ha'Ba'ah b'Aveirah. He cites the Gemara (30a) in the name of Rebbi Shimon bar Yochai which says that the reason why Hash-m does not accept a Mitzvah that comes about through a transgression when, in any case, everything in the world actually belongs to Him, is because if He would accept stolen items as acceptable for Mitzvos, then people would become accustomed to stealing even when a Mitzvah is not involved. However, the Gemara (31a) says that Rebbi Yitzchak bar Nachmani disagrees with Rebbi Shimon bar Yochai and maintains that on the second day of Sukos (or the first day of Chol ha'Mo'ed outside Eretz Yisrael) -- when a borrowed Lulav is acceptable -- one who performs the Mitzvah with a stolen Lulav also fulfills the Mitzvah. It should be made clear that Rebbi Yitzchak certainly is opposed to commandeering another person's Sukah, and somebody who does so will certainly be punished for his act. However, even though he did a sin by stealing the Sukah, nevertheless the Mitzvah he did with it is valid.

Ha'Me'or ha'Katan says that we learn from the Gemara regarding a stolen Sukah that the Halachah follows the view of Rebbi Yitzchak, and not the view of Rebbi Shimon bar Yochai.

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