\s matches any whitespace character, and a newline character is a whitespace character, so it gets matched by it (and then the whole next line is matched by ([^\n]*)).
Optionally match a plain space instead (and remove the \s from the end of prevent\s?eval\s in the first alternation).
You can also use .* instead of [^\n]*, you probably wouldn't want to match a linefeed character anyway:
^\/\/\s(prevent\s?eval|eval\s?prevent) ?(.*)$
It sounds likely that you don't want any of the \ss to match newlines in which case, replace them all with plain spaces:
^\/\/ (prevent ?eval|eval ?prevent) ?(.*)$