I think those modding down cold fjord might be overlooking some things. There is the backroom persona for politicians and there is the press room persona. Indonesian politicians are not stupid, and being not stupid they should know, even without evidence, that countries whose interests intersect with theirs, whether supportive or adversarial, will conduct espionage. They also should know that their base of power comes from a fickle and often nationalistic public whose eyes are always on them.
If we assume that the act of espionage has chilled relations, then it actually speaks of Indonesian naivety and incompetence. It is difficult to believe that national leaders, whose careers are built on guile and exploiting opportunity, would not assume the very same characteristics in their counterparts. So, what this really says is that Indonesian government leaders, fully cognizant of espionage, are doing their best to cover their behinds domestically in light of media focus and to head off popular uproar on the issue. Rather than espionage chilling relations, it is the revelation of espionage has made career-wise politicians take up a tough facade and sooth a resentful public with feigned outrage.
Think back to the leaked embassy cables a few years ago. It revealed that the Yemeni government had great enthusiasm for US drone strikes inside their borders. They were enthused for a very practical reason -- it allowed someone else to fight internal radical opposition with little cost to themselves. But Yemeni politicians could not show that face to their public, else they would risk destabilization, and so what they said to the press and to the public had to be completely different from how they actually felt.
There is more than one layer to this onion.