Of course jealousy was a motive for this letter.
But when he writes "It adds even another motive", this AVOWED motive cannot be jealousy, because it would be inconsistent with his statements at the beginning of the letter - and we can see he is anything but inconsistent.
So his jealousy was a secret motive, and he had one more (at least), and the latter was aknowledgeable to Elizabeth in the frame of this letter. It can be only, a wish to protect her.
I do think to, that he believed her virtue to be sufficient not to fall before marriage. But he did not know exactly what Wickham would accept in marriage, if somebody had given her some dowry. Mr Darcy could not be absolutely sure that Elizabeth would not marry Wickham eventually. And imagine her woe, being the wife of such a man!
Even if she didn't marry him, her heart could be broken by him in another way - remember that he doesn't know that she has never really loved him, and is no more trying to fall in love with him; his "You take an eager interest in that gentleman's concerns", and in his letter "Here again I shall give you pain.... a suspicion of their nature" to me means that he overstates greatly Elizabeth's feelings for Wickham.
So, yes, he can feel she needs protection against that man.