It's definitely nothing to do with shoes or kit. Like most marathons, London is usually overrun with Nike and Adidas athletes.
With SIS, it could depend on where she was promoting it. If she's doing so at official London Marathon events like meet and greets, then you can see why LME would be irritated. They need to sell the event to sponsors and if an athlete can just turn up and guerilla market their personal sponsors, then that affects LMEs ability to attract advertisers. It's the same logic as the Olympics but without the stupid restrictions on athletes' kit.
I thought the contractual issues could also be to do with her running Berlin so close to London. LME is paying her to turn up so they could expect her to take reasonable steps to ensure she can get to the line, which might include not running an all-out HM a few weeks before the big event.
Anyway, it's a shame we won't see her run as I think she could have done something quite special for British distance running. The British women's race is now lacking in top level quality. Jess Piasecki and Charlotte Purdue had already withdrawn, so Sam Harrison is the only person I'm interested in. I hope she can get the Olympic standard, it would be a great reward for the last couple of years of impressive progress.