The devs have essentially answered this question before.
This is meant to be a collection game. They (the devs) want you to increase your collection. That's why they implemented changes to GAC match making; they didn't want people only unlocking what was needed for meta teams and ignoring everything else.
If they gave guilds the option to constantly run DS or LS TBs, it would decrease the incentive to work on the opposing side. Don't have strong Sith or Empire? No worries! You can do LSTB all the time! Or vice versa.
Yes, it is smart to work on the strongest teams regardless of DS/LS. But TB requires you to have 4-5 teams (or more, depending on some of the restrictions for CM and SM). There isn't an incentive to work on the lesser teams that can clear waves because you aren't doing that TB.
Of course the whole reason behind all of this is encouraging players to build out many teams so they need a lot of gear. But that's how most of these games make money.
