If the sentient goo does hold memories of its past forms, then we can't hold the Doctor responsible for that. All we know is that he found it important to break the link between Amy and her avatar sooner rather than later, so that she could wake up and do what she needs to do in her real body. As for goo sloshing around in the bottom of the TARDIS, I'm sure that either the Doctor or TARDIS can hoover it out; I wouldn't let sticky floors bother you.