I was in Marsala at the end of 2012. The town is quite flat with a pedestrianised centre. I recall there being ramps at the side of entrances to public buildings and churches.
The Museo Archeologico 'Baglio Anselmi' was wheelchair friendly and all on one level once inside. The museum houses the remains of a punic warship amongst other exhibits.
I cannot help with your query regarding hotels for disabled access.
This is the comune website for tourism: