To begin with, just being placed on the wanted list doesn't make someone a 'criminal.'

Literal

In-the-first-place, wanted-listed-[just by-だけでは] 'criminal' is-not.

そもそも frames the sentence as a from-the-start reset of the discussion — 'to begin with,' 'fundamentally,' 'in the first place.' It signals the speaker is returning to a basic premise that they feel others have overlooked. 指名手配される is the passive of 指名手配する ('to put on the wanted list'); ~だけでは ('just with only ~') is a composite particle that sets a minimal condition and then negates its sufficiency — 'merely being X is not enough to make Y.' The scare-quoted 「犯人」 signals the speaker is disputing the term's applicability, not using it neutrally.