To get the obvious out of the way, "The Sea Devils" is a maritime remix of "The Silurians": from the hibernating reptilian subterranean hominids waking up to reclaim the planet from all these belligerent hairless apes, though the apes intend to preemptively exterminate them first, all while the Doctor futilely tries to broker peace between the two species. However, "The Sea Devils" notably departs from "Doctor Who and the Silurians" with how it portrays the military, in this case, the British Royal Navy, in a positive light. (For practical reasons, of course it would, since the producers secured the cooperation of the actual Navy.)
My pet theory for the early classic Who era is that the series reflects the post-WWII decline in British global hegemony, and each Doctor from Hartnell to at least Pertwee (I'm less versed in Tom Baker, strangely enough) has his own way of dealing with British declinism. In Pertwee's case, you see a once-powerful entity who was used to gallivanting around time and space (which offers a nicely literalized metaphor to the old "The sun never sets on the British Empire" saying) suddenly confined to both. Perhaps as a consequence, the Doctor collaborates most often and closely with UNIT at this stage in his history (UNIT being the stand-in for the United Nations), a collaboration which mirrors the UK's growing integration into pan-European multilateralism. (Interestingly, the UK joined the European Community, the precursor to the EU, in 1973; "The Sea Devils" was originally broadcast in 1972.)
Not that being part of an international community means that all their imperial tendencies have been quashed, however, not with the Doctor invariably trying to restrain the military's unilateral preemptive impulses and, as in the cases of the Sea Devils and the Silurians, failing to do so. But these ancient reptilian hominids are facing a stacked deck. Even the Doctor, ever the champion of a humanism that extends to non-humans, betrays his anthropocentric chauvinism when he tells the Sea Devils that they're guaranteed to be wiped out by the humans in the event of open war. With things tilted against the weird aliens and in favor of the humans (who, remember, speak with British accents), I figure that we're seeing contemporary internationalism struggling against nostalgia for Empire.
This nostalgia emerges most clearly in the adulation granted to the Royal Navy, manifested in all the loving shots of its technological might (which actually show real Navy warships and sailors). But nostalgia tends to imply a degraded present, and despite its illustrious history, the post-War Navy couldn't resist the rest of the UK's decline. In fact, by the time "The Sea Devils" was shot, the Navy was taking orders from the BBC, as a making-of featurette makes clear: the Who makers actually get the Navy to redirect an aircraft carrier to the Solent just to accommodate their shooting schedule. Maybe this faded naval glory is what prompts such conflicted attitudes towards potential threats to the UK.