Sorry for the delay on this! It fell under the radar for a bit. There have always been other small chapels and chantries in Kirkwall aside from the giant main chantry in Hightown, which was certainly the city's religious center but not its only establishment (there are way too many people for that, whatever DA2's cut-rate renderings suggested). These have continued to operate, with varying degrees of assiduousness. In Lowtown, this is fairly normal--few ventured all the way to the Chantry in Hightown anyway. In Hightown, the loss is felt more deeply. Other smaller congregations have swelled, and a couple new chapels have been built by some of the city's wealthiest families in the last decade, which have absorbed much of the remaining congregation. (They're of course also a great opportunity for them to reward their favorite clerics with positions and show off their wealth!) So things aren't being wildly neglected, but they are a lot more fractured and there's a lot more room for laziness, heresy, etc. to creep in given the lack of oversight.