Do we actually know that Excalibur is what we think it is/does what we think it does? Mostly the information is from Merlin, Arthur, Emma, and Clippit!Rumple. None of these are reliable narrators — even Merlin, who so far appears to be a good guy, clearly has his own agenda, and isn’t sharing it.
While we don’t know exactly what Merlin’s agenda is, I think he can be trusted. If he said not to pull out the sword or else bad things would happen, then Emma probably would’ve been better off leaving it alone.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy