To quote a sempai of mine: 'The only person you have control over is yourself.' Being intimidated is an internal condition; the others have taken no action against you.
It strikes me as extremely disingenuous to say that someone has had no action taken against them when they join a dojo and are told that they are welcome to train there, and then others join this same dojo, refuse to train with them because of their gender, and are indulged in this behavior. How is this any different from a passenger on the bus who is willing to sit next to anyone, but who is told by the bus driver that they may only sit in certain seats because only certain passengers are willing to sit next to them? Jim Crow much?
You can't practice aikido without a partner; if you're not willing to be a partner to everyone within the limits of your ability, you need to take your delicate sensibilities elsewhere.