I think modern scientific circles regard just about anything as a conduit for pseudoscience these days. However, I don't think holism is given any special treatment.
If you consider the ultra-pure-ivory-tower version of science, where you develop a hypothesis about the tiniest facet of the universe and then spend an infinite amount of time testing that hypothesis, then everything can be thought of as a "ground up reductionist effort" built on those tiny proven hypotheses. Real world science, however, has never been so static. There are always ideas flittering about, not yet nailed down into a bottom-up structure of theories. Quite often these ideas arise by observing gestalt behavior. Once observing these things, science then does strive to reduce it, for it is far easier to develop a scientific experiment in accordance with the scientific method if you take a reductionist approach.
However, they are very much dependent on these ideas that haven't been pinned down. They point the scientists where to go next. We may not see it much in physics, where atomic theory rules the day, but in biology there's myriad gestalt effects to consider. Over time, we try to reduce them, but there's no proof that all things can be reduced this way. Even in physics, Atomic Theory is taken as an axiom at most, and a guiding theory at least.
Consciousness is one of those things. While science may try to apply reductionism to it, so far it has not succeeded. Thus, any science which studies consciousness must embrace some level of holism because they do not yet have the reductionist structure to build upon.
Like all things, it's a balance. If science falls too far towards reductionism, it finds itself sluggish in responding to newly discovered gestalt patterns. If it falls too far towards holism, it finds it difficult to create repeatable and reproducible scientific experiments.