At first I thought he was mad but not, he burned the corpses to eradicate the virus, this is what was done with COVID19 and other epidemics,since the virus can filter into groundwater, the ground or into other areas by scavenger animals.   
  
The best way to eradicate the virus is to incinerate the bodies, and that's what he did, the rest thought he was crazy and could hurt them, that's logical, so they avoided contacting him in all those years.

  
Perhaps over the years he really forgot his real purpose and went mad, loneliness and living in that world affected him.

That's why he treats the infected like animals and doesn't kill them, although that's weird, but even stranger is that Spike didn't confront him when they left the Alpha alive, since Spike has been raised with the belief that they are bad and must be killed, that's why they are trained to shoot bows and are educated in that, so in that part he fails.

It must be said that narratively this film is very bad, but I can't stop thinking that this is the best character in the film and the one who makes the most logical sense.  
  
That is why after so many years of isolation he no longer remembers the real purpose of burning bodies, then with the bones he begins to build the monument to honor their lives, because he values ​​them and changes the true reason for the temple.  
  
That's why he says to Spike that he waited many years for someone to ask that question, but at that moment he no longer remembered the original purpose. Having spent so much time dealing with human lives, he had to create his own way of honoring them and built this monument.

Still, there are a lot of illogical things about it, like having spent so many years there dealing with infected people, making bonfires in the middle of the night attracting more attention than a firefly with the only protection being a river that an alpha has been able to cross without any problems, or having hundreds of bodies piled up in a field. I think the movie has a lot of flaws, but this character was actually very good.

I don't really know if Boyle wanted to give him that approach without saying so, because the film has many unreal and senseless things, perhaps the character hasn't even been built thinking about what I'm saying and he's simply a crazy person who liked to stack bones to make a cemetery without any sanitary intentions, but let's remember that he's a doctor.

  
salute

Dr. Ian Kelson wasn't mad, let me explain