so why was the doctor worried about the TARDIS in parting of the ways and journey's end?
Because the HADS wasn't on; he turned it on a in the submarine episode in Series 7 (forget the name) - and literally hadn't had it on since the Second Doctor, having forgotten how to do it. Thus why, continuity-wise, I think it's kind of cute.
Aside from that, there are reasons for this anyway despite the fact the TARDIS is fairly powerful & difficult to destroy or enter without specialized equipment -- he wasn't worried about it getting destroyed in Parting of the Ways, he was worried about the Daleks getting their hands on it - that's in the message to Rose... "Emergency Programme One means I'm facing an enemy that should never get their hands on this machine. So this is what you should do: let the TARDIS die. Just let this old box gather dust."
This is touched on again in Journey's End, where the 10th Doctor explains to Rose, albeit briefly, that the Daleks on Platform One and the Cult of Skaro both had access to limited tech and never could've brute forced their way into the TARDIS anyway. The ones through the Medusa Cascade had been there for ages and basically had the strength of a full Time War era Dalek army, and as such could crack into or destroy a TARDIS pretty easily with specialized equipment. So, again, that's why he was worried there. Who knows, that weird reactor area they dropped the TARDIS into might've destroyed it with the HADS on anyway.
There's a lot of plot holes in this episode, but this isn't really one of them - the HADS conclusion is lazy, but it isn't a hole.
What I really don't get is why we needed the TARDIS destruction at all. I guess so we could feel peril at the end of the episode, but I feel that the same tension could've been achieved in the cliffhanger by just having the Supreme Dalek say to Missy "We have no need your instruction" and then exterminate her and Clara, as it was. The threat then is not "The TARDIS is 'destroyed'" but "The TARDIS is in the hands of the Daleks, they MIGHT know how to get in/use it, and the Doctor is trapped a ways away with no way to get to it past the army of Daleks between him and it." Alas.