As a commercial pilot, can I fly my spouse for her work?
The prohibition you're worried about as a CPL is "holding out" flight services to the general public, which can be summarized as providing both plane and pilot as a package to strangers.

In this case, you would be providing both plane and pilot, so your concern is understandable.  However, there is a clear personal link from you to your wife and via your wife to her employer, i.e. they're not the "general public", so you're okay.  It would even be okay if your customer were a bona fide friend, rather than your wife or her employer.

If the company could rent (or otherwise provide) the plane and separately pay you to fly it, you wouldn't need that personal link.  Given you're renting from a flying club, that's not possible, but it's something to keep in mind for future scenarios.  Do check with the flying club to make sure it's okay with them and their insurer.  I assume you have the appropriate insurance for yourself.

The pro-rata stuff only applies to a PPL, and given the FAA's policy that flight time and even employer goodwill can count as "compensation" even if no money changes hands, a PPL could still get busted even if they "eat the costs" as you propose.  As a CPL, though, you don't have to worry about that, just the "holding out" rule.