If it’s too difficult to rabbit-proof your entire dwelling, I do suggest, since you care so much about Nala and her quality of life, you re-arrange some furniture so you can either create a rabbit-proof area, or set-up a large pen that can be a) temporary for when you want her inside then folded away when she’s back in the hutch or b) permanent so it’s easier to make the decision to transfer her indoors. As you realize, it’s best for her to have as much out-of-hutch time as possible, so really go the lengths to make a good space for her.
Could you perhaps use some boxes to create steps down from the hutch? The steps would lead down to an area you have penned off (so she can’t run away), then you can scoop her up in that enclosed space to bring inside.
A big part of having her inside is to try and familiarize her with the security which can come from being lifted off the ground. Naturally, rabbits do not like it, since it’s like getting swooped up by a bird; however, some rabbits can learn to tolerate it, if necessary. Familiarization can happen in baby steps, so first just getting her used to you putting your hands underneath her belly. Then lifting her a centimeter up, then putting her back down. Depending on how she handles it, you can space out sessions per day, only make sessions last 2 minutes, etc.. You want to gauge her body language, as to not hurt your bond with her.
In regards to your partner, Nala saw him as a foreign attacker in her territory. Rabbits cannot see directly in front of them either, so depending on his approach, it was probably quite terrifying since she does not know him as well. I highly suggest you being with your partner, indoors, while Nala is indoors. Rather than you feeding Nala, have your partner feed Nala treats and food. Additionally, teach your partner some of the body language you’ve learned about Nala. You being by your partner while in Nala’s presence may make her feel more secure with him around. If she’s alone with him, there is no safety there, as of yet. Also, don’t let your partner jump to interactions at the level you have with Nala. He’ll need to start with just hand sniffing, light strokes in small intervals, and limited contact-initiated-by-him. Generally, let her initiate the contact so she feels more secure.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.