I'm not really sure, but I'll take a guess
The angel was referring to the last verses of the Old Testament:
"See, I will send you the prophet Elijah before that great and dreadful day of the LORD comes. 6 He will turn the hearts of the fathers to their children, and the hearts of the children to their fathers; or else I will come and strike the land with a curse."
John the Baptist was to be viewed as the eschatological fulfillment of this passage, as you said. But what does "turn the hearts of the fathers to their children" actually mean? Well, there are some Old Testament passages that talk about how in times of crisis the fathers and the children will (whether symbolic or literal) eat each other. In other words, some people, in eschatological times will turn on their own families.
I think what Malachi and the angel were getting at is that John the Baptists ministry would also be eschatological (crisis oriented), but that he would be an agent of reconciliation rather than rebellion. Through his ministry, perhaps, fathers and children would learn to love each other (rather than eat each other!). Either people will find true reconciliation or they will find ultimate/extreme/deathly division (in other words, "or else I will come and strike the land with a curse").
The only other possible interpretation I can think of is that the 'heart' of fathers will become more childlike (in the appropriate ways) so that, through John the Baptist, people will be prepared to follow Jesus in simple child-like faith.