The goal of those sections of the agreement are to force governments to treat foreign investment the same as if it had arrived from a resident.
The intent is to stop things like what happens in South America, where they look around, see an oil company sitting there that is majority foreign owned and nationalise it to fix a balance of payments issue[2]. Some organisations (like Philip Morris) will try to use it as a hammer, but that's because anyone can sue.
The US is already party to similar agreements - NAFTA being one. They've even got a standard set of terms for them [1].
First world countries with strong court systems already have these protections in place. This is aimed at other countries who don't have quite as strong a rule of law.
As for secrecy... Just because congress gives the President fast-track negotiation rights doesn't mean that the deal has to pass. It just means that congress has to have a straight up or down vote on it, without amendments. There will still be time to review and debate it.
Agreements are negotiated in secret. Can you imagine a trade agreement negotiated in the current US Congress?
[1] http://www.state.gov/documents/organization/188371.pdf
[2] http://en.wikipedia.org/wiki/Petrobras#Bolivian_controversy