Just to close the loop on this, I called the DFO licensing office today (18775357307) to explain the situation and to find out what to do in the future if the website is down again (it is still down today). They are getting lots of calls on this issue. The lady told me that some independent access providers (tackle shops, resorts), may have paper copies of fishing licenses or may have pre-purchased licenses online for times like this when the website is down. As I mentioned above, Browns's Bay Resort did not have any paper licenses but I should have tried the local tackle shops to see if they had any paper licenses. If paper licences are not available, the lady advised me to take people fishing nonetheless and retain salmon, and if the Fisheries officers ask to see licenses, explain to them that website is down and the DFO Licensing office will corroborate that it is out of service. Having the website down does not mean that people can't go fishing - straight from the DFO.
It's not the last time this website is down over a weekend so hopefully that's helpful if anyone else is in the same situation.