And my guess is this Thomas/Tomas guy might have been Helena's monitor who found out about her being a clone, and since he was religious, he went rogue and began working against them. Other than that, I'm left with a blank, mostly because I don't like to second guess the show cuz it's just that darn cool, and my imagination never gives the show justice, lol.
Wow. This makes sense, given that the monitors themselves seem to be kept in the dark. Thomas/Tomas to Helena is like Paul to Beth. Paul didn't know what was going on until Sarah broke into his life. Looks like Paul is turning against Leekie/Dyad Institute because he loves Sarah. Tomas is turning against the clones because he "loves God."
There is the possibility that Tomas is a Dyad plant, and a fraud, Helena being used to kill clones who either are becoming ill due to their genetic manipulations (a kind of mercy killing?) or have compromised the experiment by learning of their true nature. Leekie may simply have pretended not to know of Helena's actions. I'm suspicious of Helena's "list" of clones to be killed...There's no religious reason to kill her sisters in order yet she spares "not-Beth" because she's not in sequence. That sounds to me like Dyad may have a list of clones nearing the end of their usefulness. And of course it might be a useful field study by Leekie to see if the girls can survive their trained assassin.