Are there any real counters to supers in Crucible?

You've covered the main counters, but I'll re-summarize briefly before adding the lesser ones:

1. Another Super - this usually results in simultaneous kills, but some super mechanics do a solid job at hard (or at least 'firm') countering others; very situational, only worth studying for serious PvP players.
2. Heavy Weapons/Sniper Headshots - Players under super have massive damage resistance and tend to one-shot everything, so even this can be difficult, but a rocket to the face is a bad day, period.
3. Running away - in Crucible, the most serious threat from an enemy super isn't the fact that they can one-shot you, it's the fact that if they get more than one kill, they drop orbs of light for their team... bringing their supers online sooner. This leads to what is known as the "Super Train" where teammates take turns calling their super, mowing down the enemy team, and dropping orbs to get their teammates' supers ready for the next iteration. Running away VERY effectively denies the enemy team orbs so if you can't kill, running out the clock is a viable strategy.
4. Normal weapons - Lots of damage resistance isn't invincibility. I've dropped plenty of folks out of their supers with my hand cannon. It takes a while, and they have to be asleep at the wheel for me to solo them, but it's doable. If your whole fireteam concentrates their fire, it becomes practicable even - but this requires fireteam discipline and good communication.
5. The Vorpal Perk - There is a weapon perk (Vorpal Weapon) which does (seems to be 15%) more damage to guardians with their super active.

As noted in the comments, the meta shifts, and your mileage may vary.

It's important to note that supers aren't "I Win" buttons except in key situations (match point in Elimination or Survival, for example). Crucible matches are decided by team score. Even a total wipe of all six of your team is, at worst, 18 points for the enemy team in Control - 150 needed to win. You also have supers, so the name of the game isn't "Step 1: Super. Step 3: Victory." It's also "Step 2: Get as many points out of your supers as possible, while denying points to your enemy during their super phase."