there is absolutly nothing to stop you booking a package and staying elsewhere. plenty of people do this every year.
if the reports are so bad, and there were enough of them, i would be pressing TC for a move at no cost.
which hotel is it, as others may be able to shed some more light onto the problem.
anyway, if you choose not to use the accommodation i would speak to the rep when you arrive and tell them what you are doing and check with them re details for your transfer back to the airport. if you don't tell them you could miss out on the transfer back to the airport because they have changed the time etc, but by telling them in advance they should be able to tell you where to be and where to look for changes.

I have done this a few times when I've found a package to be cheaper than flight only. I just inform the rep that I won't be using the accomodation and that's fine. I always travel to and from the airport independantly but ring the office to check return flight details.

Hi. Thanks for the quick replies. The hotel is Luabay Costa Los Gigantes and the problems have only come to light in the last 2 weeks. (Not to be confused with Los Gigantes Thomson Gold hotel which has had these issues this year and previously). I have asked to move and Thomas Cook have said they are aware of the bug in the hotel and are monitoring it but at this time they are not moving people. The problem is we go during school Easter holidays so availability, even looking for hotel only on independants, is getting patchy. There are only 3 hotels Thomas Cook can offer me but the price difference is over £1k more (we has a free child place on our original booking) so it would probably be cheaper to take the alternative accommodation myself. Transfers are not an issue as we never use them anyway and always make our own way from and to the airport.

Again, thanks for the help! Much appreciated

It sounds like the problem may be the area itself. Maybe an airbourn virus?