Kara did basically the same thing, she "found herself" in adopting the S("it's not an S"), so I don't get why this is such a problem all of a sudden.
That's not really the same thing, though, because the El mayarah (Supergirl's name for the symbol) is the family crest of the House of El, and Kara grew up on Krypton wearing that symbol on literally every outfit she ever wore, even her pajamas. Heck, since she was born about a dozen years before Kal-El, it was her symbol long before it was his.
What she ended up adopting to mirror Superman was the rest of the costume -- the red and blue color scheme and the cape. Although according to the pilot, she and Winn experimented with a range of other ideas before settling on that as the most practical, so I guess she had some ambivalence about coming too close to her cousin's look.