For your information: there are several approaches to this topic. In Japan, the high speed trains stop in the city to enable commuters reaching their destinations quickly. If this were such a major issue there would be a reconstruction already underway.
In France they apply a different approach. Here the TGV stations and tracks are moved outside the cities. This is to avoid the slow down of the trains when crossing the urban areas and using the standard tracks of regional trains. People have to use 'feeder trains' to reach the high speed train links.
So both ways are possible, both have different pros and cons. Personally I feel that a station in the Northern part (Woodlands) would be quite beneficial, together with an additional MRT link to connect to airport.