The sign has nothing to do with the charge itself. It is just a convention. Just because we write an electron's charge as $-1.6\times10^{-19}$, it does not make the electron negative or its charge to be less than that of a proton.
We could have called charge on a proton to be $-1.6\times 10^{-19} C$ and the charge on an electron to be $1.6\times 10^{-19} C$. It does not make any difference in physics. Everything will continue to work the way it should.
Saying that a proton has $3.2\times 10^{-19}C$ of charge is not wrong. However, it is more useful to refer to the magnitudes while comparing charges. I would personally prefer to say negative $5\mu C$ is greater than positive $3\mu C$ as it conveys something useful.
However, when you are using those values in mathematical equations, you need to take their sign into account. In this case, $(p^+ - e^-)$ does give you $3.2\times10^{-19}C$.