I don't know. I really don't have enough information about your situation to be able to tell how officers might view your wife's leaving Canada to stay with you during processing, but at the very least, this will set her up to have to provide proof with the application of her intention to return to Canada. It also sets up the chance of being refused on financial grounds. Even though there is no minimum income requirement for spousal sponsorships, when a sponsor is unemployed, officers are to assess the chances that the landed immigrant might have to apply for social assistance benefits during their first three years because the sponsor might be unable to honour their undertaking by providing for the basic needs of their sponsored family member, and the ap could be refused under paragraph 39 of the Act. I've seen this happen a few times when sponsors are living overseas and are unemployed during the assessment.
A39 "A foreign national is inadmissible for financial reasons if they are or will be unable or unwilling to support themself or any other person who is dependent on them, and have not satisfied an officer that adequate arrangements for care and support, other than those that involve social assistance, have been made."
A lot of this will be assessed dependent on other factors in your application: where you are from, how long the two of you have been in relationship, the quality of the relationship proofs you submit with the application, etc. For example: if you were from a country where there were cultural or language barriers to you being easily employable in Canada, there will be more concern about the fact that your wife is also unemployed. If you have been married a long time - and you have strong support for your genuine relationship - it might not be a big deal that she's left Canada to spend time with you while waiting for finalization of the application. But if doing this looks to be to add support to weak evidences of the relationship, or if you've not spent time together in the past and now she is giving up her job and home to go to be with you to help strengthen your application, it could be viewed as nothing more than a "ploy" to make it look like you are not just using the relationship to get into Canada.
I'm not saying any of this is the case - it's just that you didn't provide any info to help us assess these things, so I'm just trying to cover all the bases. At the very least, be cautious because what the two of you are planning could very well complicate the process for you.