You cannot likely "dynamically" remove tags. However with Cisco equipment I can put one untagged vlan on a trunk port. This is a trick I have used to solve different problems, such as having a management network connection to a device on the same port as a trunk on a device that forces the use of $2500 SFP's just for a 1g connection... so they typically have 1 1g port for management, but if that port is fully configurable, I use it for both.
Another problem I solved this was was when we were using a carrier's managed ethernet service to connect two buildings. We saw weird problems that only affected specific packets. We think that the vendor was basically doing VLAN stacking, and our trunk was inside of a VLAN that the carrier used to seperate customers on their ethernet. Stacked vlans allow you to support 16 million vlans while observing the 4096 vlan limit. Carriers use this a lot, but I digress. One of our authentication protocols blasted an encrypted payload that could not get a critical packet through a stacked vlan. The solution was to map the one vlan carrying that payload to the one untagged vlan on the port.
The untagged vlan on a trunk port I have heard called the "native" vlan, but I don't know if that is an official term, or just local jargon. I think this is also known as the pvid.
Many (most?) devices can't do vlan tagging, so the usual thing to do is simply put them on a port in access mode. Some devices require a special firmware load, or at least a poorly documented configuration. Most enterprise systems support vlans on some level, but may have limitations. Under linux, for example, you use sub-interfaces which usually have a limit of 255 subinterfaces. A limit usually bypassed for linux based systems controlling enterprise network appliances like switches. I think the bypass comes from not using subinterfaces, and just tracking the vlans directly in the network port driver. But now I'm just screaming like godzilla...
I just racked my switches up, I had to pull out two old servers from my home rack, I had not used them in a long time, and it was time for them to GO. Two very capable boat anchors. But I have not started the configuration, so I can't "see" your problem yet.
Ideas to solve a problem are rarely stupid.
To directly answer your question, many devices allow you to do a full trunk that includes ALL of your vlans, and a separate pvid for your vlan bypass purpose.
But if your SAN does not support vlans you should not be connecting it to a trunk port. So I'm not sure why you have this problem, unless all ports must be trunk ports. Most trunk ports support vlan filters, and probably pvid's too. So in that case, I would limit the trunk to one vlan that was either not connected to anything, or even shut down. then I would use the pvid to connect the port to the vlan you have for your SAN.
I'll be figuring out how to do all of this soon, but not today. Right now all of my windows machines in the office don't have 10g yet, and the cables to reach my wife's office has not yet arrived. She has a desktop with big storage, and a video editing system with fast SSD, so two valid machines for 10g connections to the home SAN. The 20 meter cables needed for those runs has not yet arrived, won't be here for a couple weeks, I'm guessing Amazon is shipping them out of China, based on the price I got.
I think the most I will get done this weekend is to get my NAS/SAN machines moved off the toy switches and onto the big iron, and to get one of them on 10g. The other does not have the slots for 10g, so I need to replace the motherboard with something heaftier... it's a shame, it was a sweet board for a low power 36 drive NAS but with the mini itx form factor, only the hard drive controller has a slot. I guess they aren't officially SAN's till I have iscsi mounts feeding vmware... All in good time. Basically I have dozens of systems, most are off... I'm re-spinning the home network to be a smaller stack of vmware systems, and my stand-alone FreeNAS systems.
But that means that today and tonight I will be working on the configuration, hoping I don't hit any snags. There are ALWAYS snags...