@Zachary Jensen, I would just sit down and have a conversation about it. I think it's important that spouses are aligned when it comes to real estate investing, and I think you both probably have legitimate points to make on either side, and maybe you can agree to meet in the middle somewhere.
My 2 cents, if the previous landlord raised rents 3-5% with this same tenant each year, then the expectation has been set and you likely won't have an issue continuing that trend. My fear would be that if you stop raising rents, then it sets an expectation with the tenant for what to expect from their new landlord. The justification to your wife to raise rents would be that your costs of ownership will continue to rise each year (yearly tax & insurance increases, repair/maintenance/CapEx escalation over time, etc). If your tenant stays for 20 yrs, are you going to hold their rent over that time? I'm all for helping people when they need help and for trying to keep good tenants, but at the same time most of us operate our properties for what they are, which is a business; but I think there is a happy medium that can be met between you and your wife. If San Diego is anything like Phoenix has been over the past couple years, then a 3-5% rent increase is modest compared to what the market rent appreciation has been. I don't think there is a right or wrong answer either way, just different opinions on strategy. Good luck!