didn't look really deep but saw this in save()

        $this->_beforeSave();
        if ($this->_dataSaveAllowed) {
            $this->_getResource()->save($this);
            $this->_afterSave();
        }

but there's no setter for $_dataSaveAllowed

maybe extend shipment model to add a setter for this attribute and set it to false in your observer?

I didn't look really deep, but I saw this in save():

        $this->_beforeSave();
        if ($this->_dataSaveAllowed) {
            $this->_getResource()->save($this);
            $this->_afterSave();
        }

There's no setter for $_dataSaveAllowed.

Maybe extend the shipment model to add a setter for this attribute and set it to false in your observer?