Express entry and Sponsorship are 2 different applications for PR..........your wife could apply for Sponsorship and OWP........the sponsorship will be approved based on the proof and genuineness of your marriage/relationship........Express entry profile will have no effect on the sponsorship........so its up to you if you want to delete the Express entry profile.
Although spousal sponsorship does not need a valid temporary status for approval.......your wife will need to have a valid temporary status for the OWP to be approved........it takes 4 months to approve OWP......so will advice you apply for the inland sponsorship while her visitor visa is still valid, and if possible apply for visitor visa extension if required.
Read..........
Open Work Permit denied