Unfortunately the fate of the OP's PR application is mostly up to the IRCC agent assigned to the case. If they decide against the application because the sponsor has been out of the country too long during the application process the decision would need to be appealed. Lawyers will likely need to be hired, and whether the decision is reversed or not, plan on potentially years of appeals process.
Frankly appeal would almost certainly be longer, costly, and pointless from the perspective of actually getting PR status for one's spouse [add: in a reasonable period of time].
If someone really, really wanted to make a legal point and establish some public record that it's okay to go ahead and travel and some guidelines about what 'short trips' [per the regulations] means exactly - great, go ahead - but keeping in mind that you wont' get damages, immigration appeals are mostly outside the scope of typical legal precedent, and etc. But I strongly doubt anyone is going to do so when they could just re-apply and be done more quickly.
And hence keep in mind: if appeals don't make sense, then any arguments about 'well I could demonstrate I'm really resident in CAnada and they should consider I [long list of reasons I'm reisdent even if not physically present]' are irrelevant (since you won't get a chance to argue that point).
[Leaving aside that the counter-argument from IRCC case is that physical presence is the rule for compliance with
residency obligations, and hence simple plain language reading of 'must be resident in Canada to sponsor' is that it also means
physical presence. H&C exemptions do not apply to the physical presence test - they are clearly treated as
exceptions to physical presence, not an extension of physical presence. Note, I don't mean to litigate this issue here - I'm just saying the IRCC legal position - if one chooses to challenge via appeal - is a really simple and powerful legal argument (whether or not it is a winning argument, it is one that very much
could convince a tribunal/court.]
I agree that being with your spouse while dealing with a medical issue is paramount, which is why I suggest they submit the application after the sponsor returns to Canada.
Yep. Sponsors doing so should recognize that esp with medical issues in covid times, you might get stuck outside Canada for longer. Since appeals arent' really effective in this case (as above - because other solutions better), well, draw your own conclusions.