"he sounds like he's ashamed for her and would rather conceal her nature"

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Hell ! All those years I was thinking Walter wanted JM not to be detected by Sentinels or others anti mutants devices. I would never have thought him to think this way ! I like him a whole less more all of a sudden ...

This series has so many nuances.

At any rate, perhaps a diehard Marvelite might be bothered by the X-Men redux here, but when I read this issue it didn't bother me in the least. I really liked it. I didn't see it as shortcut, I felt it served the story well in that maybe many readers hadn't come across X-Men 109 before. The familiar action served as an anchor to the story, making the new scenes surrounding the story even more exciting. The Wolverine appearance was a thrill (little did I know what the future held - that a Wolverine appearance would become such a tacky, overused device).

 I've always loved quiet, thoughtful moments with superheroes. When done well they are incredibly powerful. This is a prime example of how to pull off that kind of scene. The dialogue read and felt like a real moment between Heather and Logan, a revelation, very true to real life. Great character work in this issue.    

I think some people are missing the point.  Walter was concerned about the safety of Aurora, and was trying to look out for her. 

He was also someone who would never tolerate discrimination against mutants - but that is an intellectual construct.  Sub-consciously he does buy into the idea that mutants are somehow outside humanity, and he would be more comfortable with a non-mutant than a mutant.  Or in this specific case, someone that others would not know is a mutant.

But if you confronted Walter about this he would honestly have no idea what you are talking about and deny it utterly.  The real reason behind people's actions are always conscious.

I don't think this makes Walter a bad person - it makes him human.