Yes, any alternate option of starting their own blockchain is avoided - because it would undermine their co-opting of Bitcoin's hash-power.
It's not about hash-power, it's not that hard to make a merged-mined alt-chain which will have almost as much hash-power as Bitcoin itself.
J. R. Willett explicitly mentioned that it is important to build Mastercoin on top of Bitcoin and let them interact.
That's the key, using other people's resources
Well, if Bitcoin allows one to use other people's resource, either it is flawed, or your understanding of what it is is flawed.
The cat is out of the bag, and these guys don't understand that there are better funded players
Are you talking about something specific?
In any case, to make decentralized exchange useful, you need it to be integrated with a powerful cryptocurrency.
Let's consider an example: suppose Freimarkets got implemented overnight, and some startup offers its shares for sale through this system.
I want to invest $100k, so I buy $100k worth of freicoins... Ouch, it's not so simple: that many freicoins are simply not available on exchanges, and trying to buy them would move the price, a lot. So it isn't even funny.
Thus a barely functioning decentralized exchange which works with bitcoins is more useful than a perfect decentralized exchange which works only with some obscure alt-coin.