These aren't silly questions! I enjoy thoughtful posts that result in stimulating conversation. This is how we learn and then share what we know.

This article offered some thoughts on the nuts and bolts of why smoking might be extra bad for people with ms. From: http://aje.oxfordjournals.org/content/154/1/69.full

"How smoking may be related to the increased incidence of MS is unclear. The link might depend on the immuno-modulatory effects of smoking, although the evidence is sketchy. Different components of cigarette smoke may cause either immunosuppression (e.g., nicotine) or immuno-stimulation (e.g., tobacco glycoprotein) (3, 4). A predisposition to autoimmune responses in smokers has been suggested (34), and indeed, smoking has been found to be associated with an elevated risk of developing some autoimmune diseases, such as rheumatoid arthritis (8⇔⇔⇔–12), systemic lupus erythematosus (6, 7), Graves' disease (35, 36), and Crohn's disease (37), but not others, such as Hashimoto's thyroiditis (36) and ulcerative colitis (37).

An alternative mechanism could involve a direct effect of cigarette smoke components on the blood-brain barrier. Nicotine has been shown to increase microvascular blood flow on the brain (38, 39) and to raise the influx of permeable solutes across the blood-brain barrier in rats (40). Leakage of the blood-brain barrier has been suggested as an initiating event in the development of MS (41).

Another possibility is that some components of cigarette smoke may have direct toxic effects on the central nervous system. Cyanide, a component of cigarette smoke (42), for which levels in the blood—and levels of its main metabolite, thiocyanate—are strongly correlated with amount of smoking (43, 44), has long been known to cause demyelination in the central nervous system of animals administered comparatively large (45⇔⇔⇔⇔⇔⇔⇔⇔⇔–55), and possibly also lower (2, 56), doses. Demyelination is produced more successfully with repeated doses of cyanide than with one single, massive dose. This compound has also been implicated in epidemics of tropical spastic paraparesis (57, 58) and optic neuropathy (5, 59), diseases that share some clinical features with MS but that are characterized by symmetric bilateral symptoms and no history of relapses (5, 60).

Smoking might also increase the risk of MS by increasing the frequency and persistence of respiratory infections (13). For example, some reports (61) describe an association between Chlamydia pneumoniae infection and MS, and it has been shown that C. pneumoniae-specific antibodies are higher in smokers than in nonsmokers (62, 63). However, this association has not been confirmed (64), and the relevance of any of these or other mechanisms to the association between smoking and MS remains to be established."