Allen's position is no different than the argument against federally-funded abortions.  The idea being that individuals shouldn't be forced to directly support actions that they find morally abhorent. 

The nuance is the acknowledgement that there's room for reasonable disagreement on the topic, so you don't push to outlaw the activity outright.

Even though I'm pro-Roe v. Wade/stem cell research, I can see this as a reasonable compromise on a controversial issue. 

Of course, this position can also be seen as a politically expedient election year straddle.  Allen doesn't want to alienate his base and he doesn't want to seem too far out of the mainstream.

Also, if you want to take this line of reasoning to its extreme, you could say that people shouldn't be forced to fund ANY government activity that they find morally abhorent (e.g. some wars, all wars, health care for the elderly). 

Thats a good point, but here's the one catch. Abortion as an issue affects the mother and the immediate family alone. The reason being if you don't like an abortion, don't get one. Do those who oppose stem cell research wish to not receive the benefits the research will produce?

The strong social conservative argument on abortion assumes that a mother isn't always the best judge of a child's (fetus's) interests. 

They would say that an abortion effects the fetus (unborn child), so in a sense the impact does go beyond the mother and the immediate family.

A strong opponent of abortion will not see much difference between the abortion of a two month old fetus by a mother and the murder of a two year old.  In the second case the state has a compelling interest in protecting the two year old that trumps any rights that a family member or parent might have--so why isn't the same true for in the case of abortion.  (Once again, I don't personally hold this point of view).

Both abortion and the stem cell issue revolve around the question of when life begins.  Is it at the moment of conception?  At birth?  At the point that a fetus has the capacity to experience pain and starts resembling a baby? 

If a person accepts that human life begins at the moment of conception, then he or she is being consistent in arguing against stem cell research. 

A person who holds this view strongly would see stem cell research as being similar to the Nazi experiments on human beings during WWII (which were done in the name of scientific progress). 

From this viewpoint the question of scientific value is irrelevant.  You don't sacrifice a person's life without his or her explicit consent--period. 

Of course, if you believe that life begins at some other point, you come up with a completely different set of conclusions on abortion and stem cell research.

Personally, I'm partial to Justice Blackmun's reasoning in Roe v. Wade.  As a matter of case law, I can understand the reservations that some may have.  However, as a good faith attempt to bring some clarity to an exceedingly complex issue, I greatly admire Blackmun's effort. 

For anyone who hasn't read the decision--it's well-worth reading. 

http://www.law.cornell.edu/supct/html/historics/USSC_CR_0410_0113_ZS.html