There are two theories about this. The first is that we are in the world not of it and we cannot police every single contact we make. If their son wants to continue in the scout program, those parents will allow it on the assumption their boy will need to work with these people as adults later on, and they are right.
The second attitude is that sex perversion should not be winked at, that an adult male will have plenty of opportunities to deal with sinners of every stripe, and that youth is for growth and development, not hazardous political controversy and opinion. There is some merit to both ideas.
But the question was not about compromise or lack of that, but what should a parent do according to the Bible?
The Bible is precise about everything if we take the time to parse words thoroughly. Working with someone and fellowship are two different standards of relationship. All our relationships are at different levels.
Fellowship is, as the Bible says, sweet communion with the emphasis on the union. We do have atheists in our churches, but we don’t put them in leadership positions. We hope, perhaps, that sitting through Sunday services with a devoted wife or grandma will help them learn something. But we don’t marry them or include them in the inner circle of our lives.
Conversely the Bible does recognize that we have employment working with sometimes very disagreeable people, people we would not see after work if we could help it. Fellowship is always a thing of value; work in the world on the other hand requires us to be job oriented and nothing more. It is pleasant when the people you work with agree with your standards but if not, you can still do the job.
I worked in retail many years. You may hate God but your job here is to stack the shelves and I, as a Christian, need have no theological association with you as we work together on the job.
With that in mind, consider this scripture. “Have no fellowship with the works of darkness.”
For what fellowship has righteousness with lawlessness? And what communion has light with darkness?
Sex perversion is done under cover and often in darkness. In fact most sins are best hidden as the sinner well knows.
Personally I consider putting straight and homosexual boys together an act of child sacrifice. Kids will be faced with spiritual warfare perhaps before they even know what it is, or how to handle it. Kids have lots to do in their young lives; tossing them to the wolves is not necessary or helpful.