It's a question of economics really. If a lot of folks or businesses that might have purchased Mac Pro's in the past, now start buying laptops and iMacs with TB accessories, then, yes, the Mac Pro might come to an end. However, if enough people keep buying Mac Pro's to satisfy Apple's profitability targets for the product line, they will probably continue making them. Of course no one really knows how profitable the Mac Pro is and/or what Apple's threshold for keeping/killing it is, so one can only speculate.
It's definitely a combination of economics and shift in technology (TB + consumer parts will fill the requirements of more users than what was possible in the past), which will likely eat away at the MP's sales figures when users recognize that the lower cost iMac will fit their needs.
Yes, there may be sacrifices for shifting to an iMac for some users, but economics ultimately rule (and we're still in a recession afterall...). Those that must still have a MP, will buy one if it's still available at the time of purchase (i.e. those that cannot deal with aspects such as a glossy monitor, no PCIe slots, can utilize the additional cores of a DP system on a consistent basis, embedded GPU is too slow, must have ECC, ...).
I see this trend gaining traction in the near future as well, as consumer oriented CPU's will have 8 cores on one die according to Intel's roadmaps.
Mac Pros can have up to 12 cores, current iMacs don't have as much.
Then there are the GPUs, which are still faster than the ones you might be able to connect to a "SLOW" TB port (slow for GPUs), Then there is RAM expandability (64GB currently).
Then there are a lot more options to expand it.
The Mac Pro is still needed, and if Apple would discontinue it, several thousands of companies would lose, thus Apple would lose a lot of money.
And the Mac Pro is "cheap" to make, as it uses general parts (even expensive ones) and the box hasn't been upgraded a long time (the exterior).
Apple would be stupid to kill the Mac Pro.
But maybe they are stupid.
They're in business to make money though, just as any other company. So if the MP's sales figures drop below the threshold if it being a profitable product, I don't see them continuing with it (i.e. use it as an advertising vehicle).
They're making the bulk of their profits in other segments, such as the iDevices, and there doesn't seem to be an end to this (look at all of the recent iPhone revisions and introduction of new products such as the iPad for example).
We don't know the actual % of Apple's profit margin that comes solely from the MP, but what evidence is available, doesn't indicate that it's all that large (MP's sales figures are combined with all of the other computers <laptops, iMac and Mini>, and this combined segment of "computers" is still smaller than the device market

).
I thought thunderbolt was faster then pcie hence no thunderbolt expansion cards.
No. Not even close.
A Thunderbolt chip requires 4x PCIe lanes to transfer it's data to the system, and doesn't even utilize all of the bandwidth (TB up and down combined, is good for 1.6GB/s according to Intel <they stated 800MB/s sustained in either direction>, while those same 4x gen 2.0 PCIe lanes are good for 2GB/s).
Now consider 16x of those lanes (gen 2.0), which is good for 8GB/s. PCIe gen 3.0 lanes each provide a bandwidth of 1.0GB/s, which will increase the gap even further.
So PCIe is capable of much faster speeds.
TB is great for laptops and AIO systems that don't have slots however, so it has a potential market if it can gain traction (this aspect still remains to be seen, as it's very early yet).
But for a desktop only, it has limited value ATM. That's not to say it's useless, as it could allow peripherals to be shared with portable computers, or capture data stored on a TB equipped camera or even a smartphone (i.e. already advertised on at least one HTC phone).
name 1 thunderbolt peripheral you can actually buy today
edit: ok
http://store.apple.com/us/product/H5184VC/A/Thunderbolt
Exactly. Not many available ATM (not all that many announced yet either), are on the expensive side as well.
Also a question of longevity. 4 year old Mac Pro's can still hang. Most iMac's have fried in that timeline. Either by death to display or motherboard or anything else. Heat kills them the fastest. Apple keeps putting faster, hotter procs in them and at the same time slims them down more and more and slows down the fans to keep things quiet when you are web browsing. But when you do real work with it you get too close to thermal shutdown for my liking. This reduces the parts life even more.
I don't disagree that the thermal design isn't wonderful, but keep in mind, that Apple makes their money by selling new computers and devices.
So if your system literally breaks every 3 years or so, then users are forced to buy a new machine. Now they don't have to buy Apple, but if they're heavily invested in OS X based software, or are just "hooked", then Apple is their only alternative.
Apple may not even have a problem with this sort of scenario, and intentionally use it to their advantage.
