Use 'whom.' It's a very underused and misused word. People will know that you care about using the English language properly if you use it. But be forewarned, some people may think you're a snob if you use it. In reality, they would be the snob, and hideously rude, for pointing it out and lecturing you about it. Ignore these people and soldier on.

You can use "them" and would see it frequently. "Whom" is a bit more formal, but perfectly fine here, too.

My personal opinion is that 'whom' applies to people more appropriately.

No, you can't change it, because "whom" here is a relative pronoun of the relative clauses "all of whom had different needs" and "some of whom didn't want to be there and were causing trouble". These clauses act adjectivally to describe the forty people further. Syntactically, you can't change the first "whom" to "them", because it would render the clause independent and so you would need a conjunction (e.g. "and") to join it to the first clause. Even if you did that, and in any case in the second relative clause (which already has an "and", it would change the meaning to make those clauses further conditions for the "if" rather than modifiers for the "forty people".