First of all, it doesn’t make sense that your score would be less with your wife’s details entered. You must be missing something. You get additional points for having a spouse, you don’t lose points. See here for details. If you are not sure what to do, you should really get assistance with your application.
If you do not include your spouse in your Express Entry application, you will have to sponsor her, if you get approved. Spousal sponsorship takes a very long time – 26 months for inland, which is what you would be doing if she somehow maintained legal status in Canada. If she goes home, it’s still along application process.
However, there is a huge risk with your strategy in the addition to the fact that it’s unnecessary. If IRCC wonders why your spouse isn’t accompanying you on your permanent resident application, even though they know she’s here on a work permit, they could conceivably refuse your permanent residence application. Or worse, they could not just deny it but look into your spouse’s situation as well. If you do insist on going this way, your wife should leave Canada before you get your PR (if you get it). But don’t do that. Instead, get help with your Express Entry application.