<shrug>Being obstinate may be the end product, but it's not an intention, much less a malicious one.</shrug>
Interpreting the nature of a fictional future through its roots in the real past is an interesting pursuit as such, but it probably won't produce results that would hold up for said fictional future particularly well. If a writer has bits of knowledge he puts to futuristic use, he is likely to deliberately pervert the knowledge so that it won't be too recognizable - and when a showful of writers do the same, the only way to see any sort of continuity in it is to only accept the bits we are actually given, and to mercilessly weed out all the background bits in between. Odds of it all fitting together are significantly improved, then.
Whether a "magnetic storm" or "old impulse engines" better serve as an excuse for the Valiant
reaching the barrier is no contest, really. Kirk very well knows the ship had those old engines (or at least when the teaser starts, he already has the ship's ID down pat and has studied her history enough to get key dates right), and he still finds it impossible that she could have gone where she did. Something else must be the explanation. The storm may have done it, or then one of the half a dozen fitting phenomena from elsewhere in Trek did, or then alien intellect did. The end result? We learn that propulsion tech 200 years prior to the show was not up to the task - which is quite uninformative, as propulsion tech with those specs could range from extremely primitive STL to fairly good FTL.