It would seem then that the question raised has less to do with the nature of Milesian naturalism, as it does with the nature of science in and of itself. According to modern day conceptions of what science is and is not, Milesian naturalism may not meet the criteria; however as far as I am concerned it is minimally an early era of science.
The most basic reasoning for this conclusion is that Milesian naturalism attempts to move away from faith-based beliefs in the gods and into more structured, rational, and at least observable ways of defining every day events (as well as those cosmic events that are even less observable and understandable, such as an eclipse). While the Milesians may not be adhering to a strict scientific method, they are at least beginning to analyze the universe around them with a significantly more rational approach when compared to many of their predecessors.
When one examines science in our modern day, some millennia since these original texts were written; it is hard to tell whether or not our own modern scientific theories do much better in terms of giving us one hundred percent accurate explanations for why things are the way they are. For example, even to this day there are still some scientists who doubt theories of gravity; and feel there is more to what occurs than what we are told in grade school (“what goes up must come down”).
With that said, it is undeniable that science is not meant to be completely concrete and conclusive (though many scientists would want us to believe otherwise); as it is simply a compilation of theories based on evidence (both observable and measurable). In a similar way, the Milesians have done nothing more than provided theories as to how things work; based on their best knowledge. It would appear that even the finest scientific experiment and conclusion could still render a false result, upon further analysis and research thousands of years into the future. This is, of course, not a negative of science but rather a positive because science is often willing to adjust beliefs in light of new evidence. This is very different than faith based ideologies which frequently incorporate elements of cognitive dissonance as they attempt to connect new evidence with ancient ways of thinking.
Scientists and philosophers are very similar in that they both desire knowledge, and would rather fill the void with evidence that can be sensed; as opposed to with folk psychologies and faith-based dogma.