I would suggest that the initscript disable itself in the absence of some non-conffile file in the dnsmasq package. E.g., add a file /usr/lib/dnsmasq/package-is-installed to the package and add a line of code to the beginning initscript like the following.
[ -e /usr/lib/dnsmasq/package-is-installed ] || exit 0 The file /usr/lib/dnsmasq/package-is-installed could include a comment explaining the purpose of the file. -- Thomas Hood