you could be right and it could all be rumors - no way to tell. But Kalam was not at all a 'kiss and tell' kind of guy, so even if that conversation occurred, he would not reveal in a book; only a sensationalist would do that and he was not any kind of sensation seeker. BUT it is not impossible for me to believe that he would have been concerned about a 'foreigner' taking over the most powerful office in the country.
We all think the President of India is a useless figurehead position. But India has been very fortunate to somehow derive value out of that office. Any controversial move made by the President however rare will have the impact of a 8+ reichter scale eq! For example I don't know if you know about the time K.R.Narayanan returned a couple of union cabinet decisions for reconsideration...In October 1997, the Inder Kumar Gujral Government was forced to reconsider its decision to dismiss Uttar Pradesh Chief Minister Kalyan Singh, and in September 1998, deferring to the President, the Vajpayee Government went back on its decision to dismiss the Rabri Devi Government in Bihar.
And K.R.N was a much lower profile persona than Kalam - so imagine if Kalam (whether before or after leaving office) said any word about Sonia Gandhi ... there would be a pretty serious oiutcry from both her supporters and detractors. Being a wise man, Kalam would have kept it to himself I think, and to only those who need to know. And he knew that Presidency must be kept above politics.
Which might also be why Sonia did not support his second term.