My two cents worth!

Tom and Fredo, sentiments aside....

No doubt tough call

Tom is the intermediary So Michael uses Tom to contact Fredo after Havana does not seem to me that Tom may have had a soft spot for Fredo, definitely not after fully realising how dangerous Fredo was

Michael [and Vito] underestimated Fredo
Nobody not Michael, not even Vito had any inclination how detrimental Fredo would be, arguably even setting Michael up to be murdered, for the Donship

Tom may have preferred Fredo was spared but he was not above the Corleone ruthlessness himself including no qualms about the drug trade, Khartoum beheading, Tessio and Carlo murders

I doubt he might have tried to convince Michael to leave Fredo alone because I reckon Fredo will always be a threat and liability
No doubt Fredo's actions were continuously treacherous, his sort of deep resentment never goes away, always simmering underneath
Who wants to take on that sort of responsibility for someone like Fredo?

Anyway, I reckon Tom may have accepted, it was justified and continued to go along

He was not a wartime consigliere but even in what seemed routine matters, he was still no good, like licence for Tropigala, Geary's meeting should have been just a formality
Saying he always thought it would be Clemenza not Tessio, at Vito's funeral

Fredo made Tom look even more incompetent in not knowing about Pentangeli's survival, senate lawyer Questadt belongs to Roth resulting in Michael's perjury

Tom tells Michael "He says he doesn't know anything I believe him" Then Michael finds out from Fredo, who knew plenty including senate lawyer Questadt belongs to Roth

Tom craved, yearned to be thought of as Michael's real brother

It is difficult with Tom and Fredo as there is little interaction between them