well wow. Sounds like a real mess. Reminds me too much of our experience in May this year, attempting the same thing.
Only we never even made it to the border. We were refused visas after five days of waiting in Tam. They said that from then on all foreigners must apply for Niger visas in their home countries. This was verified by the consul himself after I asked to talk to him in private.
We later found out through a Nigerian friend that the real reason was that I had given my partner's profession as photographer. Niamey don't like journalists.

We spent the days of waiting checking everything with Niger; customs, convoys, possible alternative desert routes etc. I have a name and number somewhere of a guide who will escort tourists from Assamaka to Arlit, if it is of any use to you.

We went through Mali instead, which was exactly what we had decided we would not do. Next attempt to go Algeria-Niger is in February. But I won't even try if it will be this tricky.
One solution in your case may be to round up a number of travellers so could split the cost, if they insist. But there may not be many tourists going that direction? In May, we were the only Europeans around.

What are you going to do now? Your original visa may run out of time, and the Algerians are very strict about that.

edit: one of the precautions I am going to take is getting a double-entry visa for Algeria in case of a situation like this.
We will also get the Niger visa here rather than relying on the consulate staff in Tamanrasset.
We're flexible on time, but we won't attempt the trip unless the situation appears to be stable and foreigners can actually get into Niger.