Should we not take those verses in the historical context? 1400 years ago, when the Muslims were a budding community challenging the status quo, many rose to silence them including the Jews and the Christians. Their issue was that since they were receipients of revelation and people of the Book, why was there a need for a new Revelation that was to preserve what truth they had and correct what was not? It was a time of conflict that subsequently led to many wars. At that time, some Muslims must be desiring for finding aulia (friends, protectors, allies) from The People of The Book. They were warned not to cater to such desires because of the basic differences in ideology.
That was then. Time moved on and Muslims became a force to reckon with. They were here to stay. They were accepted by the world community. In these day, alliances are made on different levels like trade, technology, intelligence, culture and defence for common interests. If an alliance does not threaten Muslims from being driven away from their homes or lose their faith, then there is no harm provided their core values are respected.
If, for instance, India were to attack Pakistan and Pakistan needed help would it be a blasphemy to reject help from China, NATO, US or UN?
Just thinking aloud!!