I'm not aware of a method to do this within NinjaTrader. Only outside:

Probably the best/only method will be to execute an AutoIt script from within your strategy/indicator which then clicks the Market Replay window pause button at a preset location. Keep in mind, most likely, you will not be able to use the mouse when this script is executed otherwise it will fail.

Could you tell me how to call/execute an AutoIt script from within a NT strategy?

I'm not sure what you're trying to achieve so I'll put it in the context of the OP. Off the top of my head and to keep it simple...

Write an AutoIt script that checks if a file exist every n second(s). If file exist then remove file and click the Market Replay pause button. Within your NinjaScript you would just create this file when you want your AutoIt script to pause the Market Replay.

If this inter-process file-based communication method doesn't work for you then you'll want to search on how to execute programs from within .NET.