White Rose was frustrated with the delays in getting her project moved to the Congo. When Elliot announced that he had hacked the Dark Army and come up with a plan that could get the project moved to the Congo quickly, she was intrigued, and changed her mind about killing him. As Elliot said:
I pulled off something in ONE DAY that you've been trying to accomplish for months!
(Referring to his previous activities, but it does set a precedent for what he can do, when he says he can get the project moved ASAP.)
It helps to remember how important time is to White Rose. She has been known to get upset about wasted seconds and the delays in moving the project to the Congo were, IIRC, on the order of days thus far, and looking like it might be even longer.
Knowing how Grant feels about Elliot, White Rose evidently decided that his likely reaction to sparing the Aldersons (ie: complaining; butting heads with Elliot) would cause even more delays, of which she already had too many. AS White Rose says in the finale:
Your jealousy has always blinded you to Mr Alderson's value
Rather than deal with more of his attitude regarding Elliot, she simply had him kill himself, instead. It was a question of efficiency.