I don't think her motives are that sincere. She tried to distance herself from any ethnic cleansing of the Rohingya by first denying it ever happened, then reframing it as a military attack against an 'uprising' to even denying Rohingya existed followed by sabotaging inquiries and framing journalists who crticized her regime. Huge refugee crisis with rape, murder etc that she fastidiously tried to cover up. Her role was too large and consistent with her general disdain to just be considered a puppet of the military. The NLD was also co-established by former military officials so you can question how much there was a separation of powers to begin with. The relation between Suu and the military was already very diffuse with the outcome of the elections depending on that internal power struggle between the different factions.
She is not a puppet of the military. But she was a leader of a government that existed at the whime military. If she wanted to go out and say the military are evil, genocidal maniacs, they would delete her life's work of an elected government before she finished her speech. This is a massive dilemma the likes of which most of us would never have to face. Condemn a genocide and condemn your people to totalitarianism, or ethically compromise yourself and have a chance of keeping your nascent democracy. It's easy for armchair moralists in the West to opine: they don't have to deal with the consequences of another 50 years of military junta.
My point is that, all in all, whilst she made an ethically grubby choice, I'm not sure it was the wrong choice.
The NLD was also co-established by former military officials so you can question how much there was a separation of powers to begin with.
The aim of the military was obviously to create a government that could not seriously challenge their rule. They kept hold of many of the levers of power, loaded the legislature with their own appointees, and manipulated the political parties to suit themselves. Even then, the military's official party of flunkies couldn't hold the 26% of seats they needed for a majority (plus the 25% of military appointees): the minute another party could usefully stand against them in 2015 the political party of the military was annihilated in the legislature.
When in 2020 the military's pet party somehow shrank even further, the military needed to make their opinions known. They may be as crude as to just hand over power to a favoured party, or perhaps rig elections to make sure their party has enough seats, or maybe it's just a reminder to the NLD of who's boss and they'll let them back in a few months. It took Turkey 80 years for civilian government to finally defang the military. The strategy open to Myanmar democrats is likewise to tread lightly until they can gradually diminish the power of the military.