The 19th century was a fertile time for Western natural history, in large part because of the curiosity that attended their newly acquired colonial dominions around the world, especially in the tropics. Naturalists and adventurers followed closely behind the footsteps of conquering soldiers and colonists, while officials and other colonial expatriates also sent specimens back home to the museums of London, Paris, and other European capitals. In many cases, colonial administrators and intrepid naturalists were one and the same person, as the examples of Rumphius and Stamford Raffles show.
Post-colonial sentiment, however, leads many people to question the Western narrative of the “heroic naturalist” opening up new vistas of knowledge, as the writer Richard Conniff comments upon in this blog post. Were they really discovering new species, or simply claiming credit for knowledge that locals long knew. After all, many European naturalists relied heavily upon local guides and informants, without giving them due credit (a practice that has changed considerably with modern co-authorship and local collaboration courtesies).
In particular he discusses Pére Armand David, a French missionary and naturalist who traveled in Qing dynasty China and discovered (for the West) many species such as Pére David's deer, which were already known to Chinese. Is it fair, then, to call him its discoverer? Some would say to do so would be cultural hubris and insensitivity.
Part of this is to do with how we are limited by past history. Western science was born of the response of European cultures to the newfound knowledge of the world beyond its borders. Its conceit of being universal is partly a historical accident, of being at the right place at the right time, so to speak. The fact that most of the modern world puts Western science in a privileged position as an explanatory framework through which to view the world is part of that historical accident (though see this article for a rejoinder). Now that it has been so widely adopted, to call it “Western” science might no longer be accurate or honest. Calling the European naturalists of old “imperialists” might be true in individual cases (many of them were certainly serving imperial projects or believed in the imperial cause), but to reject their science on these political grounds is a non sequitur.
In some cases, their work helped to preserve local knowledge that might have been lost otherwise (ironically through the socioeconomic change wrought by colonialism). I'm reminded, for example, of I.H. Burkill's monumental compendium, Dictionary of Economic Products of the Malay Peninsula, wherein he recorded many traditional uses of the seemingly innumerable plants, animals, and natural products of Malaya. With development, the traditional strand of transmission for this knowledge between generations has been broken, leaving those of us who are interested to have to acquire it from the written record. Hence the standard Malay dictionary in Malaysia, the Kamus Dewan, frequently refers the reader to Burkill's work and those of other colonial-era writers in the definitions associated with plant names, simply because that is the textual record that we have.
So yes, I would say that many naturalists were imperialists, but we should disentangle their imperial legacy from their scientific one. We can't correct the political injustices of the past, but their documentary record of the lost, rich world which we have lost continuity with can help us recover that heritage and begin to appreciate it again.