Since the creatures attack physically, the easier solution would be to have numerous cheap "poison" autopiloted ships filled with (antimatter or insert nastiness here) that kill the things when attacked. Smash the hull and the antimatter containment fails; BOOM. For that matter, it's not a bad way to drive evolution. If all human ships blew up this way, humans ships would be like poison caterpillars. Eventually you select for creatures that don't attack humans.

"They are very aggressive .... They attacks ships". You answered your own question.

@DWKraus Yup. I'm picturing a story where the defense against pirates was nukes with deadman switches. I forget what bit of technology caused that.

You mean like in Star Trek: TNG's episode Galaxy's Child?

You say that "no one found out what is the chemical composition of their body because, when they die, their corpses kinda disintegrate." In the real world, things don't disintegrate. Especially in space somebody should be able to collect chemical samples from the area around where one of these creatures has died.

10km is very short range for space

50 to 100 km is nothing in space (lets say, rounding error when triangulating position from visible stars will be muuuuuuuuuuuch bigger then negligible 100 km) Also, heat doesnt move nor exists well in vacuum (there isnt any material to bring the heat from one point to another), so 3000/5000 K hot sphere isnt really gonna work just like that...

@TomJNowell I wrote 10k km, let me write 10.000 to make it clearer

@Jan'splite'K. The 50 to 100 km sphere is only to make it more dangerous to people who want to kill this creature in close combat. Also there are a lot of science laws that doesn't work in my fictional universe, the propagation of heat in space could be one of them.

Why are they "whale shaped"? That's a shape that makes sense for animals living in a sea. (If the out-of-universe reason is "Because my story is about space whales", one reason to hunt is because the human is "space captain Ahab", perhaps. Maybe space- Moby Dick is as intelligent or more than a human. I'd read that story.)

10 thousand km is more like it :) and still rather up close-ish in range but on a space scale. The Dr Who episode on space ship britain might provide useful material

As to the whole heat not moving in space that is easily addressed by saying the release electromagnetic radiation instead, which does propagate in space and can transfer enough energy to be dangerous, though you may want to pick a wavelength, I'd probably stick to microwave or higher. That being said there are allot of issues with thermodynamics here, these creatures are expanding way more energy then they would likely be able to take in. I assume you're writing softer sci fi where you don't care about that though.

@DWKraus just a nitpick, but I doubt that what you suggested would have a large evolutionary factor in changing the behavior of the creatures. Evolution does work like that in general, but any creature that lives 1200 years must reproduce very infrequently. When you have to wait many hundreds of years between generations it's going to take too long for evolution to really change the creatures psychology much. Our tech would likely evolve to the point the whales are no longer a risk before the whales evolved to avoid us.

Please drop the "only one organ" description. It is nonsensical. Everything in a body counts as an organ. Your skin is an organ, as are your bones. Your whales have senses since they can detect things. Those senses must involve some sort of organ. They can reform themselves. That involves some sort of muscle organ. They can think, at least at a stimulus-response level. That involves some sort of brain organ. Humans may not be able to recognize or understand these organs, but they exist. You don't have to change your whales to fix this, just be more careful in how you describe them.

You will need physics quite different from our own. You can't grow such a creature from starlight, since 1) creating matter from light creates an equivalent amount of anti-matter 2) the required energy is huge. It's also pretty weird for a species which collects energy from light to be semi-transparent, since you can't collect light that isn't absorbed. Another issue with normal physics is that the bubble of heat will need a medium (e.g. plasma), since you can't just heat vacuum.

Because we’re humans. Killing things is what we do.

"move at 500.000 km/h - die of old age (~ 1200 years), starving (they can live without “eating” for 10/15 years) - they can “jump” for a few seconds at light speed." - Alpha Century is 4.37 light-years away. I didn't do the math but I'm pretty sure y'all ain't gonna make it. Space operas require FTL travel.

How about making them tadpole shaped?

A hard to kill species with no apparent use for its remains? Dude, do you know how much a steak of spacewhale is gonna fetch at those new fancy 20 star restaurants?

@PaulSinclair For an example of macroscopic organisms without differentiated organs, see sponges. It is possible that the whale is made of a continuous tissue that evenly distributes all functions throughout the body. Such an being would be described as organless.