| Yes, a Jedi Master should use Force Storm. A Jedi Master should use every tool at his/her disposal. Even a LS Jedi Master can wield DS powers like Force Storm with little difficulty. As a Jedi Master, you'll have ample FP to throw around on stuff like this late in the game. With a huge pool of FP and a very modest FP Regen (some of the Force Forms give you plenty) you'll be a powerhouse. My suggestion is as a LS Jedi Master you pick ONE or maybe TWO lines of DS power and fill them to the max. I like Force Wave, Stasis Field, and either Force Storm or Death Field. Push them back, freeze them in place, and then either blast them to bits or suck their vitality.
As a Jedi Master, you should have your WIS pumped through the roof (30+) so your DC to resist your ranged attacks will be pretty obnoxious. You should have your CHA pumped up too (20+), and at that point there isn't enough of a penalty for throwing "opposite side" powers to worry about. So then it just comes down to a choice between the LS Master bonus, the DS Mastery bonus, or the Neutral "name crystal" bonus.
Yeah, the neutral name crystal might be a bit more powerful than either the DS or LS versions, but you also don't get a DS/LS mastery bonus. Factor that in and LS/DS is better than "neutral".
I always build Kreia as a pure-dark Sith Witch with maybe one LS power (Heal is nice). She's my "DS designated hitter". She never gets very good in melee, compared to your other options, so I think she is best held to the back as artillery and kept on "droid/jedi support".
I don't think TSL is really intended to be finished as a Neutral. You're supposed to pick sides early on. You either help the Council, or you kill the Council. You either help the Exchange, or you fight them. Thats how Visas comes in. Thats how you deal with Korriban.  | 
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