Using pre-existing music used earlier in the series was and is a common practice in any TV show. TOS did it all the time, and it only had a couple of years worth of music to work from; There's eight years of Murray Gold score sitting in the vaults at this point. At any rate, I don't think the tracking hurt the episode any - at any rate, the music wasn't as In Your Face as Gold's score usually is.
It's more forgivable when it's a TV show and you have to get them cranked out on time. When you're doing it for a major motion picture (the Star Wars Prequels, for instance), THEN the "lazy/cheap" charge sticks.
The whole "Thomas Thomas" sequence felt like filler to pad out a too-short episode and give Strax something - anything - to do. Which doesn't exactly bode well for The
(prospective) Vastra and Jenny Adventures.