Why did Braxton force Chilton to commit suicide in The Accountant? Since Lamar was behind the embezzling, Chilton is not guilty...or was he complicit with Lamar in the embezzlement?
Lamar was behind the embezzling, but one of the main things about getting away with a crime is to not be seen as having committed the crime.
Lamar allowed the accountant to look into the incongruity noticed by Anna Kendrick, in a faux show of openness about his business. When it was clear that there was a kind of embezzling going on, the accountant was shutdown before he traced the source.
With just enough proof that there was malfeasance but not enough proof to explicitly link it to a culprit, Lamar's sister pointed the finger at Chilton. Braxton was called-in, the accountant was shut-down, and Chilton was forced to commit suicide out of guilt.
The film doesn't go into much detail, but it's possible that Lamar's sister was overzealous and that's why she was subsequently murdered, as well. Lamar might have been upset that she immediately accused his life-long best friend, and yet because he knew he had to hide his crime, he let Braxton intimidate Chilton, but then also had Braxton kill his sister as recompense.
Chilton and Lamar's sister were both innocent, seemingly, and it's Lamar who was embezzling the funds to devalue his company before taking it public, after which he could reinvest the stashed funds and create an inflated sense of cash influx in the company, instantly upping the stock value and emulating rapid capital-growth which would further inflate the stock prices and create more (symbolic) wealth for the stock holders -- himself included.
It is possible that Chilton and Lamar's sister were in on this plan, and Lamar ultimately had them killed because word was potentially getting out and he wanted to eliminate everyone who knew (the accountant and anna kendrick, included) before going public with the company stock ... but I think either way, Chilton committed suicide because Braxton intimidated him with threats against his family. Guilty or not, Chilton chose suicide over any possible harm against his wife and family.
We don't know what happened with Lamar's sister, but it's likely that she too was being exposed or framed for a role in the embezzlement, without mentioning the embezzlement.
Lamar clearly can't explain his cash reflow scheme, otherwise the whole plan is pointless, and framing somebody for something that you don't want people to know, is equally pointless. So, it's likely that they weren't complicit, and were just complacent. They didn't notice the descrepancies, because they relied on their accountants. Until Anna Kendrick noticed, and then it all became real to everyone. Lamar could have been doing this for years, but because they might have been small enough investments, he was able to hide everything, until the accountant came along and made all the connections.
Aware or not, Chilton recognized that he had no way out of the situation with Braxton, so he choose the means of least pain to his family by killing himself and saving them from experiening and witnessing torture.