I have a similar situation, with 2 unspayed females living outdoors. Unfortunately, they couldn’t live inside even if they were perfectly litter trained, just because they shed to badly and my mother cooks for other people outside our household. Litter trained or not, though, they are allowed to play in our basement, as long as I clean up after them. I have decided to spay them in spring. Back to your situation, I think spaying would be a great idea, given the fact that there is a very high risk of reproductive cancer in unspayed females. Plus, it would make less cleaning for you and she could very well live longer. As to her getting scared, she could end up having to go through surgery anyway to remove a reproductive tumor if she is not spayed. As to them getting to come indoors, then yeah, that could have the benefits of better protection from thieves and predators, plus a closer relationship with you. But you should be very careful of indoor dangers too. i.e. poisonous houseplants, exposed cords,  and other family pets. (She would need to stay inside for 1-2 weeks after her spay anyway.) Ever if your bunny is in a pen and not free roaming, which is perfectly fine, they could jump out of the pen and get into things. Other pets or even small children could get into the pen and hurt them. These dangers are all avoidable, so just use common sense. You might be surprised at how high a little bun can jump. Parsley is 3lbs. 12oz. and she can clear a 28in. fence! Regardless, spaying is your best option here. 🙂

As long as you have a quality rabbit-experienced exotic vet whom you trust to do spays, I 100% recommend having your female rabbit spayed. It is clear you care about her quality of life, and getting her spayed is the #1 preventative measure you can do to prevent uterine cancer. Intact female rabbit reproductive systems are constantly undergoing hormonal fluctuations which impact the cell growth, thus contributing to a very high likelihood of cancer formation. To read more about uterine cancer in female rabbits, see here: https://wabbitwiki.com/wiki/Uterine_cancer

In addition to eliminating cancer risk, it also contributes to a more stable, secure bond between your two rabbits.  There is absolutely a chance that by going to the vet and getting spayed, some tension may arise from the new smells she has incurred at the vet; however, her no longer being hormonal means the relationship between her and your male are no longer subject to the unpredictabilities that may come from one or the other being intact.

Keep in mind that it is impossible not to stress our rabbits. We induce stress when we clip nails, groom them, handle them to examine them, etc… what matters is whether that stress is warranted, and when it comes to vet visits for a spay vs. an emergency spay due to seeing signs of uterine cancer, the stress of a spay definitely is preferable.

Spaying a female is a more invasive procedure than neutering males yes; however, as long as you have an experienced rabbit exotic vet, a spay is a routine procedure that countless female rabbits have done and live wonderful lives afterwards. It is important that your rabbit is given the “green light” from a competent rabbit vet to ensure the highest chance of recovery from the procedure. See here for more info: https://wabbitwiki.com/wiki/Spaying_and_neutering

Yes, spaying is more invasive. But it’s definitely worth it in the end. As Wick said, it is a routine procedure. Just make sure you are comfortable with your vet. Ask them questions about their experience and success rate.