An editorial in the Dawn also said that the joint statement issued after Kerry's three-day visit indicated that both countries had Pakistan in mind when they referred to the need to eliminate "terrorist safe havens".
The daily said it was clear there were irritants too in bilateral relations including over America's surveillance activity and trade issues.
"That, in spite of these stumbling blocks, the two governments should express the kind of sentiments they did at the conclusion of their fifth strategic dialogue highlights the deep understanding they have developed on a number of issues," it said.
This, Dawn said, included America's assurances to the Narendra Modi government to support India's inclusion in the UN Security Council as a permanent member.
"With corporate America keen to do business in a market as large as India's, Kerry's visit signals an end to whatever reservations America had about Modi's record as Gujarat's chief minister.
"Islamabad, however, must take note of those contents of the joint statement in which America and India have not minced words and have shown an extraordinary degree of understanding on matters concerning Pakistan.
"The call for speeding up the trial of the Mumbai carnage suspects was coupled with a dig at Islamabad."
The daily that while Pakistan may have its own concerns about such views, the fact is that the Lashkar-e-Taiba (LeT) -- blamed for the 2008 Mumbai terror attack -- was a proscribed group in Pakistan.
"This reality alone should compel the state to expedite the trial of the Mumbai suspects.
"Indeed, cracking down on militant groups is in Pakistan's own interest and should not be linked to attempts by New Delhi and Washington to develop a relationship that, despite the hurdles, may in the long run alter South Asia's geopolitical contours."