If you don’t need to use CSV package in particular, with readdlm from DelimitedFiles you could do
readdlm(filename, Int, skipstart=2, comments=true, comment_char=';')
It will read anything after a ; character (included) as a comment and skip it.
I don’t know much about CSV but it seems it to have optional arguments for comments that you might try to use in the same way: Reading · CSV.jl
Although here it says that the comment character should be at the start of the line…