I have Moorish swords, too, and I know they are really heavy and have a wide blade, which makes for an ouchie head. Double blades on the head in one spot will hurt, yes. If you are not wearing any headwrap, it will also break off lots of little hairs until you have something like a buzz-cut on top.
Can you wear a headband or a light head wrap? That will help. You can also make your hair into braids or tie it back to make a pad of hair on top. Second, you can keep the swords in place for a short while during the dance, then move them. Try one on balance and manipulate the other sword, or balance on on the head and one on the palm, for instance. Know that when you practice, you usually have the sword on much longer than you will when you actually perform, so you probably get sore. You may choose to wear a wrap for most of the time while you practice.
Your head gets somewhat used to it, after a time, yes, you may get a sort of callous. And you will probably develop a little divet in your head.
One more thing about the Moorish--it's meant to be a two-handed sword, so be careful not to torque your wrist trying toone-hand it. you might try balancing the Moorish first (two-handed), while the baladi sword is on the floor or on a nearby table, or with a troupemate. Then dance a little and then retrieve the second sword. The baladi can be manipulated one-handed with ease.
And hey, if you are not ready to dance with both swords at your performance, just use one until you can get very confident. One sword done very well is better than two done not-so-well.