I wouldn't characterize it as fear, per se? Viola's not scared of Alec, she's just realistic. And thorough. By the time Isabelle left, she was aware that to lose Isabelle would make Alec very unstable, and she planned and prepared for that. One such way she did was killing Maggie Beth, to help make sure that instability wouldn't be headed straight for her like an oncoming train.

If Alec did find out, I would say Viola would probably have about six months of hell on earth before death by vivisection. As always, I gesture to @underground_ira and their wonderful fic A Family Portrait, which depicts their very accurate take on what Alec would do if Viola tried to separate him from Isabelle in a much less drastic fashion. Take that and multiply it, leave it in a bucket of gore to putrefy for a while, and you'd get his reaction to learning what Viola did in canon. (Fic linked in replies)