Two things:
1. Contributions
I agree your ability to contribute additional funds is limited. You can overcontribute if you want to meet the deficiency, but you'll pay an excess contribution tax of 6%/year on that amount until you forgo making that much in normally allowed contributions down the road. This isn't prohibited or disqualifying, just moderately expensive, and probably the right choice for a deficiency that's up to a few times the $5500 annual contribution limit.
In addition, if your IRA goes negative, it's not clear to me, absent a right of offset for you having personal non-IRA assets held with the same broker they can seize, that the broker has legal recourse to your personal funds in this case. They could sue your IRA, but if it's broke that doesn't get them anything. They could sue you, but you aren't guaranteeing the IRA (that's not allowed, and it's a separate legal entity anyway), so I would suspect they would have a hard time winning. They would have to argue there is an implicit guarantee that everyone has to backstop their IRA, which would be a prohibited transaction even if it wasn't invoked, so all IRAs should be invalid. I don't think that would fly...
2. Prohibited transactions
It's only prohibited to borrow or extend credit to an IRA under these rules if it's done by a
disqualified person. That list includes the IRA owner, most immediate relatives, and any fiduciary to the IRA. Fiduciaries here are people given investment discretion over the account, so your broker, unless you're letting him make discretionary trades in your account or paying him for investment advice, would not be disqualified. In short, having an unrelated third party like your broker make an arms length non-recourse loan to your IRA is not a prohibited transaction. Examples of this already in common use involve IRAs owning investment rental properties and getting a mortgage.
https://www.theentrustgroup.com/investments/real-estate/strategies/non-recourse-loans
And a cautionary article from one of the IRA experts still mentions IRA loans are allowed under appropriate terms and conditions:
https://www.financial-planning.com/news/steer-clear-of-these-taboo-ira-investments
"When an IRA needs to borrow funds in order to purchase IRA assets, that loan must come from outside financing, without a personal guarantee from the IRA owner."
I guess you should to read the margin agreement for an IRA very carefully to make sure you weren't making a personal guarantee by accident, but I doubt a broker's lawyers would let them write that into the contract since it would blow up any IRA that agreed to it even if it wasn't used.
