IE Plugin normally uses less bandwidth than Ajax so if it is possible try that since it will potentially improve performance. If you need Ajax and this is the only option then you may need to tweak your webserver. Are you using QlikView Web Server or IIS?
the other thing is to evaluate what you are trying to show in your table. Will a user really need to see thousands of rows in a table? Is it something they should only view by a selection made elsewhere (e.g. only for 1 customer at a time)? If so, consider a condition on the calculation.