Minerva hadn't only made her suggestion of Legilimency because it made sense, but because she wanted to see his reaction. She knew he was a changed man, but she wanted to see how much he had changed. The mere suggestion of using Legilimency on his wife disgusted him.
"Severus, it's your choice in the end," Minerva reminded him kindly.
"I know that. And my decision can't be the use Legilimency on her. She'd never trust me again--"
"If she found out," Minerve interjected.
"And she would find out. She's a clever little witch." Minerva was almost shocked to hear genuine fondness in his voice.