Clearance is not the most pressing issue you are likely to have.... I'm 5' even, so I know how hard it is to find a properly fitting bike. Unless you are quite long in the torso/arm, at your size, I would think it very likely that the bike is also too long for you.

Do you find that you have to stretch to reach the handlebars? (can you have a comfortable bend in your elbows or are your arms pretty much straight out) Did they have to put a ridiculously short stem on it (like a 50 or 60cm) to allow you to comfortably brake and shift?

I'm surprised that the shop steered you to that bike..... there are smaller models, usually designed for women in the same price range. 44 is generally the smallest size for anyone but custom makers (or kids frames), but not all 44's are made the same (the only mfg that I know who does a stock 42 is Pinarello, and that's just the way they measure, their "42" has the same geometry as other's 44's.....) A bike like the Specialized Dolce in a 44 is smaller all around with a greater stand over clearance because it is a compact frame. Even Bianchi makes a women's model, though their lower end is a bit more expensive than the bike you purchased.