It sounds to me as though he doesn't trust her to take her pill. Maybe she's wobbling, and he senses it…..perhaps there have been some false alarms and he's feeling vulnerable.
We are always being told that if men don't want to be 'trapped' into fatherhood and don't want to support their own unplanned children then they should take responsibility for their own fertility….and he has. Good on him.
And let's not ignore the fact that many women in LTRs who are already using BC themselves do not actually want or appreciate their partners using 'belt and braces' condoms as back up anyway, and can often seem quite offended at the idea that someone else should be taking control of whether they can get PG or not.
I see no issue with what he has done whatsoever, PROVIDING he isn't be dishonest with her about his long term intentions. After all, it doesn't really matter what she might want, does it? He doesn't owe her anything except honesty about his position on having children. If he has continued to be absolutely clear on that then he has nothing to feel guilty about.
She's welcome to leave if the situation ceases to suit her. The fact that he now cannot get her PG shouldn't really need to come into it. If she chooses to stick around in the hope that she can trick him or manipulate him into becoming a father against his express wishes then more fool her.
On the other hand, if he knows or suspects she has changed her mind and he is planning to string her along for a few years with vague promises to 'think about it next year' then shame on him. That would be a despicable thing to do.
But based on what we know so far, he has done nothing wrong in my eyes. For both their sakes though, it would be better to be straight with her about what he's done. It doesn't bode well for the level of trust in the relationship that he should seek to keep this a long term secret on purpose.