FinCEN seems to think it is. Per the guidance you linked to.
An exchanger is a person engaged as a business in the exchange of virtual currency for real currency, funds, or other virtual currency.
Now it is important to remember that "guidance" isn't new law. It is suppose to clarify existing law. Normally it is used in cases where "Z" is regulated, a company is doing "X" AND "Y" which together is not material different then "Z". FinCEN releases a guidance advising that they consider "X" + "Y" the same as "Z" and thus law/regulation 123 applies even if a company isn't actually doing "Z".
In this case Bitcoin is a square peg. FinCEN looked at all their regs and they don't have a square hole. They have the MT "hole" but it is round. The guidance is trying to force Bitcoin (square peg) into Money Transmitter (round hole). Per the guidance FinCEN is indicating they interpret existing law to define exchanging virtual currency for another virtual currency as money transmission because it is a "value that substitutes for currency". This makes "logical" sense because that is their rational for why exchanging of virtual currency for real currency is money transmission.
Since guidance isn't new law, the existing laws on which FinCEN is providing "guidance" on can be found here:
Electronic Code of Federal Regulations -> TITLE 31--Money and Finance: Treasury -> CHAPTER X--FINANCIAL CRIMES ENFORCEMENT NETWORK, DEPARTMENT OF THE TREASURYhttp://www.ecfr.gov/cgi-bin/text-idx?SID=4ed28aff321d97007276a7736cae032e&c=ecfr&tpl=/ecfrbrowse/Title31/31cfrv3_02.tplTo narrow it down further.
This is the section of the e-CFR on MSBs:
http://www.ecfr.gov/cgi-bin/text-idx?c=ecfr&SID=00fd89174701c0486dc0ca18ba1d033f&rgn=div5&view=text&node=31:3.1.6.1.6&idno=31This is the section of the e-CFR with general definitions:
http://www.ecfr.gov/cgi-bin/text-idx?c=ecfr&SID=00fd89174701c0486dc0ca18ba1d033f&rgn=div5&view=text&node=31:3.1.6.1.2&idno=31The later is important because the general section defines key terms on things like "money", "transmission", "MSBs", etc.
At the federal level there is no MT license, or specific MT registration. There is only a MSB registration. When you register as an MSB you indicate the reason for MSB registration. MT is one of those sub types. A company declares all the regulated activity they are engaged in and as such a company can register multiple sub types.
Now there is also the question on if a virtual currency <-> virtual currency exchanger is a money transmitter under STATE law. However get ready for reading thousands of pages of regulations if you want to dive into that one.
1) FinCEN definition only apply to federal law.
2) No two states have the same definition when it comes to the key terms of "money transmitter", "money", etc.
3) Most states probably don't even know the answer to the question at this time.
4) The exact nuts and bolts of the how the exchange works will determine if that specific exchange meets the definition of a MT under any state law.
5) The bad news. Even if you DON'T meet the definition of a MT under state law that doesn't mean a state won't incorrectly determine that you do and at that point you need to have a plan on what to do.*
* In our case VA believes our company is an issuer of stored value which is regulated under VA law. We believe we are not. It isn't that we don't believe issuers of stored value aren't regulated under VA law it is that we don't believe that our economic activity meets the statutory definition. That belief plus $5 will get you a cup of coffee though. Either we need to (expensively) convince the state, or (more expensively) fight the state in court, or (even more expensively) accept the incorrect determination of the state and get licensed. Even if we prevail it will be an expense incurred and a loss of revenue while we resolve it. Business owners should keep that in mind. You can be "right" and it still be very disruptive and expensive to get the state to accept that you are right.
Ultimately what matters is what a judge thinks and you should approach it from that direction. If you think reg "X" doesn't apply and FinCEN thinks reg "X" does apply then eventually (it may be a month or a decade) you both will end up in front of a judge. If a judge agrees with you then FinCEN "guidance" is moot. If a judge agrees with FinCEN then you are probably have already (past tense) broken the law and are looking at civil and criminal liability. "Guidance" is simply FinCEN way of saying "
we see it this way and when we take you to court this is the arguments we will use to convince a judge that your activity is regulated". It is possible that FinCEN guidance is wrong and they will lose in court. IMPORTANT: be sure you grasp the risk and the implicit unfairness though. If FinCEN is "wrong" they don't lose anything (except some taxpayer money). They either write some new guidance or they ask Congress to pass some new laws because current ones don't cover virtual currencies. If you are "wrong" then you potentially could lose everything, your savings, your livelihood, your good name, even your freedom. Eventually most of these issues will end up in court but there is no real case law on Bitcoin or virtual currencies yet. In thirty or forty years this will be old news (like all the regulatory and legal issues related to non-bank entities and credit cards are now). Bitcoin isn't just cutting edge technology it is cutting edge application of law and that means risk, complexity, and uncertainty.
DISCLAIMER: I AM NOT A LAWYER. THE ABOVE POST IS INFORMATIONAL ONLY AND SHOULD NOT BE CONSTRUED AS LEGAL COUNSEL. IF YOU HAVE A SPECIFIC QUESTION ABOUT YOUR ACTIVITY YOU SHOULD RETAIN INDEPENDENT LEGAL COUNSEL. 
