Yes, your boss should pay you.
You are describing a commercial photography shoot that will produce photos for a commercial use.
Since you are in Canada, contract, licensing, releases, etc info from the ASMP may not be all that helpful.
The way commercial photography work is priced you would charge for your time and talent (a Creative fee), and a separate charge for use licensing of your copyrighted photographs.
I am not familiar with Canadian 'work for hire' (WFH) statutes, but I do know that Canada made some major changes to their copyright laws in recent years so they more closely gibe with US copyright law.
In the US, a statement in an employment contract saying "performs additional duties as required" would not be sufficient for an employer to claim copyright ownership of photographs made by an employee whose normal job duties do not include doing photography. Even if you did the shoot during your regular work hours does not automatically make it a WFH situation here in the US.
In the US, for WFH to be in effect, both parties (employee/employer) need to sign an agreement stating that WFH applies.
A use license would define that the use of your photographs would be restricted to just 1 media type - the clinic's web site.
The use license would define what maximum size (pixel dimensions) your photographs could be used at, and for what period of time.
Use licensing of a photograph for clinic web use only (at up to 400 x 400 px) would be about $35 a month - per photograph.
If the clinic uses 10 photos, the monthly use licensing fee would be $350 for all 10 photos.
Instead of a monthly rate you could charge a yearly rate and give a discount for a 1 year use license.
One photo @ $35/month would be $420 for a year of use. So you could discount that to somewhere in the $350 to $400 range, per photo, per year.
If the clinic uses 10 photos that would be $3500 to $4000 per year for the use of 10 photos on the clinic web site.