For me the issue is not meaning vs structure, since these are really two faces of the same phenomenon.
Rather the issue is the pedagogic sequence from instance to system and vice versa.
Since meanings and the structures that realise them only occur in texts, our approach starts with whole texts, in which learners encounter instances and gradually accumulate systems.
Using a simple technique of guided repetition we can teach beginning learners to read and say a short text within an hour, and then use this as basis for focusing on particular features. As they acquire fragments of systems these can be used to illuminate new instances and so on.
In SFL, meaning and structure are not "really two faces of the same phenomenon", and structures do not realise meanings. Rather:
(1) Meaning is a stratum in the hierarchy of symbolic abstraction. What realises meaning is wording, not structure.
(2) Structure, on the other hand, contrasts with system. The distinction here is axial: between the syntagmatic and paradigmatic axes, respectively. What structure realises is system, not meaning.
meaning is realised in wording (stratification)
system is realised in structure (axis)
system on the stratum of meaning is realised in system on the stratum of wording
structure on the stratum of meaning is realised in structure on the stratum of wording
system on the stratum of meaning is realised in structure on the stratum of meaning
system on the stratum of wording is realised in structure on the stratum of wording