As a 1st dan in chang hon ryu Tae kwondo, I am going to sound a little biased. Although, like previously mentioned, it all depends on what you want out of your training. In both Tae kwondo and Kickboxing (like all martial arts), there are good schools and bad schools.
Now, what you determine as "good" or "bad" all depends on what your goals are. As in, there's not much point in joining a school where lessons are more focused on fitness, if you're aiming to acquire self-defence skills, and vice versa.
I do however agree, that since becoming an Olympic sport, Tae kwondo has "softened". Now, this all depends on if you do WTF (South Korean government/Kukkiwon approved) (the style seen on the Olympics, and the more popular version in the US)
Or if you do ITF style ("founded" by General major Choi hong hii 9th degree blackbelt).
The WTF style is more sport orientated, whilst ITF is more "traditional". As a ITF -based - but not affiliated Jeja (taekwondo student), I can't say what does/doesn't go on in a WTF school.
There are bound to be good WTF Sabumnims out there who teach practical taekwondo, as well as the "Mc-dojo" type people, readily available at a strip-mall near you. Avoid those people!
I admire the way in which Muay Thai is trained, as it is less "safety concious" compared to modern day TKD.
It's funny, cos in reality, within the ITF (chang hon) patterns (hyungs/tuls/forms/kata) low kicking, throwing, chocking, gouging, maiming, scratching/clawing is all part of the applications.
Though, I think that's where TKD is let down (in my personal opinion). Not enough emphasis is placed on contact work, like how you'd do "sticky hands" in wing tsun and things.
TKD is a bit of a pioneer martial art, as it mixed General Choi's experience in Shotokan (he got to 2nd dan I think, correct me if I am wrong) with Taekkyon, Su bahk, Kwon bop and a little Hapkido. It's a shame that people forget it was a art that was feared in the vietcong for being lethal and brutal.